So it isn't suspect when a team ALWAYS has more energy than the other after 90 minutes, but it is when a team does it once in a high profile game? Like "everybody knows United work really hard, so that's not suspicious, but if a team outworks them it is"? Both teams could well have been at it, probably have it institutionalized at the team and in their leagues. Maybe Athletic were peaking more, maybe United were motivated less, maybe Athletic were just the better team on the night.
The player you mention I think was Íñigo Pérez, though. He came on as a sub with 10 minutes to go.
Nevertheless, Athletic (hardly anybody calls them Bilbao) are one of the few teams with a sanctioned doper on the squad (Carlos Gurpegui served a two year ban for nandrolone in 2002, which was fought and fought; it took about four years to get him sanctioned).