The class was empty when Sam shrank. The teachers were probably infromed of Sam's clothes lying on the floor as soon as the next class started. But the news didn't reach Ashley-and thus Sam- the very same day, because the clothes weren't discovered during lunch time and after that AShley attended a class and went straight home. Sam was never seen naked. The only thing out of the ordinary was some pieces of clothing at his lab station. 

They did, however, find all his clothes -underwear included- lying in a classroom, and he wasn't seen changing in the shower or at the gym. So, given his rebelious nature,  they came to thet conclusion that he'd probably been up to no good, like going on a naked streak. it was "the only possible explanation" according to Sam himself.