It sounds like we've said this for the last several years, but Sweepstakes in general seemed to be at the less "on-the-ball" and more "make things up as we go along" end of the spectrum, so it's not too surprising if judges prep was incomplete. Of course, it's been so long since a notably well-organized one that current students have no point of reference.
I too am uneasy about the precedent. Correcting a clerical error, like a typo'd time that results in placement change, seems like the right thing to do. Going back and reviewing footage days later to find uncaught violations to get the result you want is clearly not desireable. In this sport, there's no time pressure to make an instant judgement call - if anything's questionable, flag it for review and get it right. This isn't a "what's a football move?" ambigious decision, it is a black and white call that the judge missed (or missed recording) in real time.
It sucks for Spirit to have to return a trophy they thought they had, but it also sucks worse for Apex to not get the trophy they actually earned. Apex is probably busy enough racing to not pay attention and record every infraction that anybody ahead of them committed to make sure the judges noticed - that's the judge's/sweepstakes's job.