There's no mention of this anywhere online...
although that doesn't mean that it didn't happen!! Brendan Fraser and Chris O'Donnell are both noted as having shown their rears in the shower scene, while Matt Damon is noted as having shown his rear and 'a flash' of pubes. The movie was originally rated PG-13 by the MPAA, and no alternate versions or cuts have ever been submitted for review, with the grounds for the rating given simply as 'language'. Britain's BBFC has likewise passed the film as PG on three separate occasions (theatrical, video, widescreen video), with no variation between any of the versions, and no substitutions noted.
http://cndb.com/movie.html?title=School+Ties+%281992%29
HOWEVER... I will never say never... especially if the sequence in question is
extremely brief and may simply have passed reviewers by.