Marcelo Bielsa kept it up for 90 minutes. He squatted in the left corner of his technical area, got up, paced across the turf and squatted in the right corner of his technical area, got up again, paced across the turf again and squatted in the left corner of his technical area, pausing en route to take in the view from the middle. Standing this time. Over and over again. Every few seconds. Up, pace, down; up, pace, down; up pace, down. A different perspective, a better view. Except that it made no difference: whichever way the Athletic Bilbao manager looked at it, this was terrible. Truly awful.

Monday night at the Vicente Calderón and on 20 minutes, Bielsa saw Atlético Madrid's striker Radamel Falcao glide past San José and dink it over Gorka Iraizoz for the first. On 42, he saw Falcao replicate that Johan Cruyff goal – or this Fernando Torres goal, or this Ismael Urzaiz one – by leaping in the air, side on to goal, foot raised half way to the crossbar, to volley the second. On 58, it was three, all of them for Falcao, and on 84, it was four. It should have been more: Gorka Iraizoz made a handful of superb saves. Atlético Madrid had 14 shots on target; Athletic didn't have one.

"We were," Bielsa admitted, "impotent in the face of the dimension of our opponent." The dimension of that opponent was gigantic: Arda Turan was consistently dangerous, Falcao's brilliance was barely believable and Atlético had destroyed Athletic in last season's Europa League final too. Bielsa talked of "antagonistic styles" and took the blame for not devising a strategy to impose upon Diego Simeone and his team. But it was not just about Falcao or Simeone or Atlético; there was something else, something deeper, something a little depressing. Something in that word: impotent.

An inescapable feeling that Athletic Bilbao, the team that reached two finals and destroyed Manchester United at Old Trafford, are unravelling before his eyes.

Athletic Bilbao are bottom of La Liga. It is only week two and last season Athletic suffered their worst start in 32 years but became possibly the most exciting, most different, most enjoyable team to watch in Spain.

There are three other teams with no points and a long way to go; Bielsa's done it before too. This summer, they had three players at the Olympics and two at Euro 2012. It was, some say, bound to take a while to re-find their feet and their fitness. They'll come good. But Athletic have conceded nine goals already and it just doesn't feel right.

As Athletic's players filed out of the Calderón late on Monday night, the last of them leaving the car park just before 1am, Javi Martínez and Fernando Llorente were not among them. Both have told Athletic that they don't want to continue. Martínez is waiting for a deal to be concluded with Bayern Munich, who have offered €40m (£32m). Llorente, whose contract is up at the end of this season, will not sign a new deal and wants to go to Juventus. Fans have whistled and booed him at training sessions and graffiti has appeared on the window of the club shop. But despite standing to lose him for nothing, Athletic are refusing to sell, pointing at his €35m buyout clause. The window is closing. In the meantime, he's not playing.

It wasn't supposed to be like this. They call Bielsa El Loco. As Iker Muniáin put it, he is not as mad as people say, he is madder. But he was also brilliant: he had revolutionised the team, changing the club's entire identity. They were fun. They reached two finals. They lost them both, completely running out of energy as the season entered the final weeks, but afterwards the fans chanted for the coach to continue. He was the architect of a new era. He was also non-committal. It took him a week to decide. There was a barely disguised panic: if Bielsa goes, we're screwed.

When he did finally announce that he was staying there was relief. Athletic's project would continue and so would the players. But Bielsa's methods are wearing and the fatigue, both mentally and physically, among the players is real. His relentlessness has proven successful but it can also be enormously stressful.

In early July it took a turn for the surreal. Bielsa called a press conference which lasted almost an hour and a half to announce that he had filed a formal complaint with the police … about himself. He gave a statement in which he admitted to having insulted and pushed the site manager on the works being carried out at Athletic's Lezama training ground. He said he had shoved the site manager out of his office after promises made about the completion of work were not met. "I'm sorry," he said, "he may well be the worst site manager around but he deserved respect."

Bielsa had a point: the work was not completed on time, leaving Athletic without the facilities that he had demanded ready for pre-season training, the club had done little to push it through, and he was forced to act in the name of the club, having given them a four-day margin to sort it out. (And who in Spain hasn't felt like clobbering a construction company once in a while?) But he had also revealed the difficult relations that exist between him and the president. Athletic responded by publishing a statement in which they insisted that they "do not share at all the personal and subjective opinion expressed by Marcelo Bielsa", claimed that the work was being carried out "correctly", and pointedly referred to him as an "employee of Athletic Club".

Bielsa opened a Facebook account to reply, point by point, to his club. "I can accept that they have said I do not have the authority [to act as I have], but not that, directly or indirectly, it has been suggested that I have not told the truth," he said. "My opinion about the quality, progress and the control and fulfilment of the work carried out at Lezama is not subjective. I can prove that each and every one of the things I said corresponds to concrete and verifiable facts … if no one made mistakes, why does the first team not have a place to carry out its pre-season in the timeframe agreed? … Why is it that the club and I see the same reality in different ways if we both work with good intentions for shared objective?"

"This," he says, "modifies our relationship."

A sense of unease has taken over, a feeling that something could break any moment. There is tension in the air. When Athletic signed Aritz Aduriz and Ismael López, Bielsa had no qualms in pointing out that he had not asked for either or them. And as the season drew near, both Martínez and Llorente, Athletic's two best players, expressed their desire to leave. Team-mates understand their decision but there is irritation at how late it came; the season is two games old – two defeats, nine goals conceded – and still there is uncertainty.

Bielsa says he has asked Martínez and Llorente if he is the problem, implicitly posing the solution: "If you're going because of me, I'll go first." He says they are not, but there has long been a private recognition that Bielsa and Llorente have important differences. This is an opportunity for them to move while they have suitors and lots of them: last season was probably unique and Athletic's absence from the Champions League weighs heavily.

The bottom line for Athletic is clear: these are their best two players. Last season, Llorente scored 16 league goals. No one else got more than six. Another team debilitated. Every side in Spain that qualified for Europe has lost players this summer. And the fear now is that the departure of Martínez and Llorente may lead to others following suit. Even the €60m they stand to raise is no comfort. Because of their policy of signing only Basques, the pool of potential players is limited. In transfer terms, the money is almost worthless. The Betis midfielder Beñat Extebarría is the most attractive available player but Bielsa is not interested. On Monday night, he said he did not see the solution in signings. He needs to find it somewhere.

"Of course I'm worried," the coach said, "It's impossible for a team like this to be in the position it's in and not be worried about it."

Talking points

• When Florentino Pérez arrived in the directors' box at the Coliseum, it all looked so very good; by the time he departed again, it all looked so very bad. The TV screens in the front row were showing the game from Pamplona, where Barcelona – apparently playing in Sunny Delight bottles – were losing 1-0 to Osasuna. Their play was almost as bad as their kit, too. Beat Getafe and Madrid would climb back above their rivals. But Leo Messi scored twice – that's four for the season already – to rescue Barcelona and Madrid blew a 1-0 lead to lose 2-1 in front of less than 10,000 fans. That's three games without a win at the start of the season for Madrid – something that has never happened to José Mourinho before – and a five-point gap between them and Barcelona. Yes, it's early but considering that Madrid only dropped 14 points in the whole of last season it is significant. The performance was, Mourinho said, "unacceptable".

• Valencia won on Saturday, Deportivo won on Sunday and the aggregate score was a draw. 3-1 up at half-time, which ended at midnight, Valencia conceded two second-half goals. Half-time team talk? Tomorrow is another day?

• It's a Barcelona-Madrid one-two at the top. The Madrid team in question, though, are Rayo Vallecano – two wins from two, they sit second, thanks to a brilliant performance of a Leo of their own. This one's Brazilian and only started playing 11-a-side football a couple of years ago.

• Falcao: wow.

• Málaga-Mallorca: pyjama party.

Results: Real Sociedad 2-1 Celta Vigo, Betis 1-2 Rayo Vallecano, Espanyol 1-2 Zaragoza, Málaga 1-1 Mallorca, Osasuna 1-2 Barcelona, Getafe 2-1 Real Madrid, Granada 1-1 Sevilla, Valencia 3-3 Deportivo, Atlético 4-0 Athletic, Valladolid 2-0 Levante.

• Latest La Liga standings