It doesn't have negative consequences when a girl catches the MC with another.
When Emma hears the MC carrying Martha to her room (unavoidable) she only gets angry because her plan of going upstairs to lose her virginity didn't work, not because the MC is cheating on her (he's not, as the MC and Martha aren't in a relationship). That will create some dynamics between Martha and Emma.
Right now, the known relationships are (shadowed what you haven't played yet):
Eileen knows about Erika
Erika knows about Norah
Alexia knows about Norah
Scarlet and Daphne know about each other
And no one has shown any problem with it. My Dorm is a game where you can pursue every girl without bad consequences in the long run.
The time jump is still a long way off
Thanks for the answer, I knew it wouldn't be permanent but the scene where Erika finds out about Norah had me kinda scared