This may not seem an acute crisis on the level of (God forbid) spectators being injured or a major doping scandal, but the damage to the key stakeholders could actually be deeper and longer-lasting.
At the time of writing LOCOG had cleared the early reputational hurdles with alacrity. Danny Boyle's opening ceremony was a quirky triumph, the transport system in the early days was free-flowing, entry to the venues was smooth and friendly.
So it must have been a major blow to LOCOG comms director Jackie Brock-Doyle to notice how many events looked distinctly underfilled.
To its credit LOCOG moved swiftly. Within hours of the media running the 'empty seats' story, Lord Coe was telling broadcast outlets his team was 'investigating' the problem. Soon afterwards LOCOG had identified the absent members of the nebulous 'Olympic family' (governing bodies, media, accredited associations) as the main cause.
Importantly this comms tactic cleared Olympic sponsors of blame. These key funders of the Games have unfortunately become easy scapegoats for anything that detracts from public access and enjoyment.
By Monday LOCOG had moved to fill the empty seats, having first brought Culture Secretary Jeremy Hunt on board, with fast turnaround sales to the public. The positive story led London's influential Evening Standard that day.
As I write, the agenda appears to have moved on. But the empty seats problem could easily raise its ugly head again.
It is potentially critical precisely because of all of the good work that LOCOG has done so far. Having overcome the problematic ticketing process last year and successfully whipped the British public into a supportive frenzy via the Torch Relay, it is devastating for we punters to see empty seats at top events.
Many of us bought tickets for early rounds of obscure events on the acceptance that it was a simple problem of oversubscription. Indeed, that's the media line that Lord Coe took during the ticketing problems last year.
But if thousands of dignitaries who have been offered seats simply can't be bothered to turn up, then the problem is instead one of misjudged allocation strategy.
The ultimate success of London 2012 will be that it is perceived as a 'people's Games' with a healthy-looking legacy. Only then will LOCOG's team deserve their well-earned rest.