I think it sounds just like what it was. Casey spent the night with her boyfriend and the roomie didn't notice if she was in his bedroom or if she was already gone when he left for class.
Why would she change her pattern? She was spending the nights not dropping by for booty calls up until that time. I believe she stayed.
The question as to why Clint didn't speak much to Tony was because he (Tony) was spending his time with Casey at that point when he wasn't working. This happens frequently with new couples and friends. They get so involved that friends take a backseat for a bit.
He didn't say why he no longer worked at Fusian after that.
Seriouslysearching, what do you think happened?