I've seen this happen on a few occasions. As Drew indicated, it's likely that the beer moved on to a mini BOS round where it was edged out by other beers with comparable scores. I've judged some mini BOS rounds with 4-6 beers that had resulted in the higher scoring entry finishing less than 1st place.
Judging during a mini BOS round doesn't take into account the original scoring as a basis for awarding 1st, 2nd or 3rd place in a category. The judges may or may not be aware of the original scoring. The only information they are given is the style, subcategory and special ingredients if applicable.