Beyond the sideshows there came a moment that briefly reminded those present what they are meant to be here for. Mohamed Salah’s relationship with the crowd inside Cairo International Stadium is intense enough to transcend description. Nowhere in the world does an arena hang on a single player’s every action quite like this. So, when he scored Egypt’s second goal against the Democratic Republic of the Congo on Wednesday, the roar confirmed something genuinely special had passed. It told that Egypt’s icon had risen to the occasion and suggested this Africa Cup of Nations might, too.

Yet the sense of privilege, that feeling of fuzzy warmth simply to be watching, paled quickly. A masterstroke from Salah was welcome after a difficult few days’ teething problems for the tournament but could be tainted beyond repair now Egypt’s players seem hellbent on stoking a scandal that threatens to drain the colour from any future flourishes their demigod might produce.

Had they accepted the Egyptian Football Association’s (EFA) decision to cut Amr Warda from their squad amid allegations that he sexually harassed women online, perhaps waiting to see the outcome of any investigation into the player’s conduct, then few would have debated their stance. Instead they pressed concertedly for his reinstatement, with Salah’s voice discomfortingly prominent, and the EFA announced early on Friday that Warda will be available for their last‑16 tie this coming week.

Salah had called for Warda to receive a “second chance” and his thoughts clearly held more weight in the EFA’s eyes than the sensibilities of the millions who accept Egypt’s society has a deep‑rooted, perpetual problem with sexual harassment and abuse. A UN study in 2013 found 99% of women in the country had been affected. In trying to sweep the issue under the carpet the players have created a tornado and one wondered what they were thinking on Friday afternoon when, with hashtags like #nationalteamofsexualharassers and #salahsupportssexualharassment gaining huge traction on social media, they appeared to double down with a joint statement that was removed within two hours of its release on the EFA’s Twitter account.

It included further quotes from Salah, Ahmed Elmohamady, Ahmed Hegazy and Aly Ghazal – the first apparently acknowledging Warda’s mistake but saying his future “needs to be saved” and the last three seemingly citing a “malicious plot” against Warda – but was replaced by a “disclaimer” that said the comments’ publication had been “a mistake”. Perhaps someone had finally seen a modicum of sense; whatever the truth, it emphasised that a manageable situation has become a mess.

The point where everybody would be better off saying nothing has long since been passed and the reaction when Egypt face Uganda on Sunday, in front of what ticket prices dictate will be a middle-class and largely social media-literate support, will show how far the issue has tainted perceptions among a populace that prides itself on placing football ahead of almost anything.

That is what Salah and his teammates appear to have done and it was a particularly risky move for the Liverpool player, who is rarely outspoken or, indeed, spoken against in these parts. In tweeting his support for Warda’s rehabilitation while stressing that “‘No’ means ‘No’”, he was trying to be statesmanlike but ended up equivocating and, by extension, endorsing. Salah’s intervention was clumsy rather than malign; then again, it is about time that was eliminated from any form of discourse as a valid excuse. And would he have felt compelled to write those words if the alleged offences had occurred in a Liverpool context, rather than one in which Egypt cannot be seen either to fail or be disunited?

It is the dominant story in a tournament whose start has been troubled in other ways. When Algeria played Senegal in Cairo’s 30th June Stadium on Thursday night, a potentially dangerous crush at the gates resulted in supporters flooding in without security checks and, in some cases, vaulting the turnstiles. Four years ago 20 fans died in a stampede outside the same venue. It beggars belief that a repeat could be threatened again, particularly given that Egypt’s traumatic recent history around stadium violence extends much further, and the local organising committee was unable to provide the Observer with an explanation – or any assurances that future games there, including a semi-final, will be safe – at the time of going to press.

Other matches have experienced the opposite problem. The Confederation of African Football’s drive to create a more “European” standard of administration has included a Fan ID scheme whose applicants must pass rigorous security checks. Anecdotal evidence suggests many have been unable to purchase tickets even after receiving their Fan ID, with no provision for smoothing things out at stadiums that are all but empty when a north African team is not involved. One team were distressed to learn that players’ families, many of them having travelled thousands of miles to see sons and siblings compete at the pinnacle of their careers, were marooned outside the stately, 1920s-built Alexandria Stadium during their opening match. Those of a cynical disposition suggest the authorities, in a country where the state is smotheringly present at every half‑turn, are quite happy not to see big crowds gather on a daily basis during a month when the former president Mohamed Morsi collapsed in a courtroom and died.

That has not stopped instances of mild, irrepressible protest. In Egypt’s fixtures, and at some of the better-attended games involving their rivals, local fans have held their lit-up phones aloft in the 20th and 74th minutes, marking the tragedies at 30 June Stadium and in 2012 at Port Said, where 74 died. It can be perceived as a quiet way of saying no one will ever forget what happened, nor the deep‑seated and unresolved grievances.

These episodes are far more serious than the chaos the international media, some of whom did not receive the accreditations requested months in advance until several days into the tournament, walked into before the opening game. But the fact this was due, at least in part, to a crash in Caf’s computer servers raised obvious parallels as well as a wry laugh or two. Caf, stricken to the point that the Fifa secretary-general, Fatma Samoura, will be parachuted in to apply emergency surgery later this summer, remains in an unholy mess. If a tournament is only as good as the confederation hosting it, then this Cup of Nations, seemingly cursed from the moment of its original awarding to Cameroon, would be unwatchable.

It is a good job, then, that the early on-pitch standards have been encouraging – even during an enervating group stage whose length makes a keener focus on extraneous issues inevitable. Players have generally coped well with the heat, although FifPro, the global footballers’ union, was forced to write to Caf after planned water breaks were applied erratically over the opening week. The pitches have certainly seen plenty of hydration: these are the best, smoothest playing surfaces seen at a Cup of Nations in years and the impact on the spectacle has been inescapable. Favourites such as Algeria, Nigeria and Morocco have already shown their hand while Madagascar have been a surprise package in all but sealing a last-16 place and games between underdogs such as a thriller on Thursday night between Kenya and Tanzania have generally been exuberant fun.

Egypt have contributed on that front too and, if they proceed to win on home turf for a third time, the slicing run with which the winger Trézéguet eviscerated DR Congo’s midfield to create that goal for Salah will bear replaying over again. What a shame, then, that far less savoury memories will linger, too.