There were just hours to go until Real Madrid's match against Athletic Bilbao and Madrid were about to finish the first half of the season five points clear at the top of the table with 16 wins in 19 games. Favourites to win the title, they were about to score their 67th goal and Cristiano Ronaldo would soon be on 23, one ahead of Leo Messi. But it was not about that all that. Not now and not later. It would not even be about the 4-1 win – a brilliant game, open, exciting and end-to-end, between two sides that can be great to watch. The focus was elsewhere. Even José Mourinho's focus was elsewhere. The team meeting at Madrid's Mirasierra Suites Hotel wasn't so much about formation as about information.

Mourinho wanted to know one thing above all and he wanted the players to know that he would find out. Who had plunged the knife in his back? Who had leaked a conversation from the training ground? Who was the mole? Mourinho claimed to have banned newspapers from the team hotel – "there is internet, you know", one player said with a smile later – and insisted that he had not read Marca on Sunday morning, but of course he had. Few coaches are so aware of the media as Mourinho, a man with his own press officer, a man who is delivered a dossier of cuttings every morning; one for whom the message is part of the match. Mourinho had read it, so had everyone else and it did not make for happy reading.

Marca's cover showed Mourinho and Sergio Ramos face to face. Word for word, they reproduced a conversation between the two men, and Iker Casillas, at Real Madrid's Valdebebas training ground on Friday morning – two days after Madrid, playing ultra-defensively, had again been beaten by Barcelona; two days after Ramos had noted: "We follow the coach's tactics. Sometimes it works and sometimes it doesn't." According to Marca, the conversation started with Mourinho turning towards Ramos and saying: "You [plural] killed me in the mixed zone." To which Ramos replied: "No, mister, you only read what it says in the papers not everything we said."

Mourinho replied: "Sure, because you Spaniards have been world champions and your friends in the media protect you … and because the goalkeeper …" At that point there is a shout from Casillas, training 30 metres away: "Eh, mister, round here you say things to our faces, eh!"

Another part of the conversation starts with Mourinho saying: "Where were you on the first goal [against Barcelona], Sergio?"

"Marking Piqué"

"Well, you should have been marking Puyol."

"Yes, but they were blocking us off [using basketball style screens] with Piqué and we decided to change the marking."

"What? So now you're playing at being coach?"

"No," replies Ramos, "but depending on the situation in the game, sometimes you have to change the marking. Because you've never been a player, you don't know that that sometimes happens."

Suddenly, the lid had been lifted. Just a little, but lifted. The conversation – which was impeccably polite, Ramos even using the formal form of "you" – revealed Mourinho's irritation at the Spaniards and his belief that they are protected by the press; by extension, it hinted at his suspicion that they are the ones responsible for the leaks to the media – this report came in the context of a year in which El País's Diego Torres has written a number of stories about events within the dressing room and in a week in which Marca had correctly reported that Angel Di María would miss the clásico, despite the coach's attempts to keep that quiet.

From a player's point of view, it revealed the one flaw in Mourinho's long career: he was never a player. Somehow, he just doesn't know what they do. That is a feeling exacerbated by a mutual lack of comprehension, a sense of distrust and division, and by poor results against Barcelona. It also revealed something else, one of the greatest obstacles that Mourinho has encountered: Madrid is not Inter or Chelsea or Porto, the Spanish media are not the English or Italian media, and Spanish players are not the same as English ones, or Italians or Portuguese. One of Mourinho's greatest and most often lauded skill – dressing-room relations – has not been as easy to apply here.

It was not just the story itself that was interesting but the fact that it was published, how it was published and when it was published. After all, other stories have been written before. They were more easily (which is not to say honestly) dismissed; this story was not. The detail, the precision in the quotes, the specifics of it; the fearlessness with which it was put out and the silence with which it was met. Context is key, especially when the relationship between certain sections of the media and certain parts of the club is so instrumental. The shift was palpable. Columnists who were among Mourinho's most aggressive defenders had repositioned themselves. In the aftermath of the Barcelona defeat that was always likely. After Pepe's behaviour in the clásico – and the laughable, hostage-style video apology he was obliged to offer up on Thursday – it was more likely yet. But still the move was telling, hinting at a political realignment. And for Mourinho, that could be the most worrying thing of all.

Throughout Sunday, the story was chewed over; fans debated it, the media too. Not just the comments on the cover but the ones inside: the player complaining that Mourinho will not let them talk; the player insisting: "you got annoyed with Iker because he apologised to [Barcelona's] Xavi [after the Super Copa clásico], but what did Pepe do in that video?"; the player complaining that "it's impossible to win a game with eight defenders". The day before, El País had reported on the tensions between Mourinho and some players over the tactics; some players demanding a more expansive approach, Mourinho reproaching them for doing so.

The tension at the hotel grew. So, everywhere else, did the theories. It was hard not to go all conspiratorial. Who could it have been? And was Mourinho barking up the wrong tree? He was not the only one turning detective; everyone else was too. The assumption that it absolutely had to be a player seems flawed. Players have friends and agents. So do managers. And teams have people around them. Lots of people. Clubs do too, at all sorts of levels. Information is delivered in various forms and the form here was telling – this did not smell like whispers but something much more tangible. Marca's presentation of the conversations suggested not just that they had a story but that they had the proof that they had a story. Madrid, a club usually quick to deny, said nothing. After Sunday night's game, Mourinho would refuse to deny it. Three players would come out with the exact same phrase: "We're not here to say whether it's true or not." Anyone would think they are told what to say in the mixed zone.

Madrid versus Athletic Bilbao was presented as a plebiscite. On defeat to Barcelona. On Madrid's image under Mourinho. On the division – on whose side you were on, players or coach? On the signings, now down to Mourinho and of which only the substitute José Callejón has really succeeded. On Mourinho himself. By Sunday night, some at the Santiago Bernabéu decided, quite rightly, that the crime was not so much the leak as the content of the leak: the tension inside the dressing room, the defeats, the image of the club. And who was responsible for that? Mourinho. The question was what would happen next, where would this end?

The game was scoured for clues – was it significant that Ronaldo turned and gave Xabi Alonso a look that could kill? – and so was the starting lineup. Every action was analysed, counter-analysed and, let's face it, probably over-analysed. Mourinho left out five players who had played against Barcelona. Coentrão, Pepe, Carvalho, Lass, Higuaín, and Altintop. He included six who hadn't played against Barcelona: Ozil, Kaká, Marcelo, Arbeloa, Varane. Even Esteban Granero got a game. The lineup could not be any different; the polar opposite of what Mourinho had done in midweek: for virtually every hard-working but limited player taken out, a talented ball-player had been put in. You could see meaning in everything. Three Portuguese players had been taken out, two Spaniards put in. This was the team that some players had apparently demanded.

Had Mourinho given in? Or was he sticking them on the pitch knowing that it was almost a no-lose situation for him: if Madrid won, they won; if they lost, he could say: "see, that's what you get when we play your way." Had he also prevented the players from "making the bed" for him? They couldn't very well effectively down tools and turn him over precisely on the day that he did what they wanted. Or was he simply preparing for Wednesday night when there would now be no option but to attack Barcelona? Mourinho, normally so active, only left his bench once in the entire game – a game that had five goals, two penalties, a red card, and a couple more penalty shouts. Was that a clue too? Was he fearful of how the fans might react to him? Was he hiding? Or trying to keep a low profile? Was he trying to show his disconformities with the side he (?) had chosen, a kind of "this is your team, not mine"?

Or was he, as he insisted afterwards, just so confident that he never felt the need to get up and correct anything? Even though Madrid went 1-0 down and Athletic were the better side for the first half an hour.

There were many questions and few answers – least of all from Mourinho. There were, though, hints. Glimpses of a guerra civil. No more than hints perhaps, but hints nonetheless. When Granero was taken off on 72 minutes, the player who more than anyone else represented a shift in approach – the Madrid that Mourinho had turned his back on and some Spaniards had wanted – got a massive ovation. And then, with 10 minutes to go, it happened. The fans who had chanted Mourinho's name all season – something that has never happened for a coach before – chanted it once more.

Well, some of them did. More of them did not. In fact, they did the opposite. The Ultra Sur began chanting Mourinho's name. And the rest of the stadium – 30%? 50%? 80%? – whistled their disapproval.

It was not so much an attack on Mourinho per se as an attack on the decision to chant his name, to do it now, in this context, and with this backdrop. It was a symbol of disapproval of those that did so too – the Ultras who had chanted "Pepe, kill him!" and "Journalists, terrorists!" Divisions at Real Madrid had been laid bare. This time among the fans. And there was no escaping that there they were: whistles. Win on Wednesday and all will be right with Madrid's world again; Mourinho will be a genius again. Now, he is not. This has been perhaps his most difficult week as Madrid coach. Not that he admitted as much.

"Difficult? Why?" the coach asked. "I lost a game on Wednesday, I prepared one on Friday. Today we won. Tomorrow is Monday. Why is that hard? It is the first time that I have been whistled but it's not a problem. There is a first time for almost everything. If I had been whistled at Chelsea where they don't even whistle the opposition manager, it would be a problem. Here they whistled Zidane and Ronaldo and now Cristiano Ronaldo. This stadium whistles the best in the world – why shouldn't it whistle me?"

Talking points

• Messi: bloody hell. He'd only scored once away all season – now he has scored four times thanks to an astonishingly good hat-trick away at Málaga. AS gave him four stars (well, aces) out of three, while Roberto Palomar in Marca finally saw sense and said: "there are no longer any words, except swear words." Holy shit, for example. Messi now has 22 goals for the season. Ronaldo has 23. Carry on like this, and they'll both break the goalscoring records. Again.

• Goodbye to the best flat top in La Liga: Granada have sacked slightly bonkers coach Fabri. Which may make Granada better side – or, let's face it, it may not – but will certainly make them a less fun too. Not so much on the pitch as off it.

• The Simeone Effect keeps on keeping on – Atlético won at Real Sociedad on Saturday night, their first away win in eight months. That final Champions League place is not as silly as it sounds.

• At last, the Seville derby was back. Good too.

Results: Real Sociedad 0-4 Atlético, Betis 1-1 Sevilla, Espanyol 3-0 Granada, Racing 1-2 Getafe, Osasuna 1-1 Valencia, Rayo 0-1 Mallorca, Málaga 1-4 Barcelona, Levante 0-0 Zaragoza, Madrid 4-1 Athletic