Not sure what competitions you've judged in, but the one in question specifically has 3 bottles per entry to cover things like this. Granted there was something wrong with my sanitation procedure for that bottle, but for any competition with more than one bottle per entry, there is no reason NOT to try another bottle when scoring an entry. It's not like the infected one is going to BOS. Maybe the competitions around here are run more efficiently, but it shouldn't take all day to judge a flight and then do BOS, and the incidence of infected bottles is generally quite low in every competition I've judged.
Of course if you've got 20 beers in your flight it's another story, but for an average flight what difference does it make? Set that bottle aside, judge the next beer, then come back to the infected one later.