I think the break up makes sense (although it is annoying!). When they get back together at Uni they don’t put any labels on their relationship. Niall asks Connell if Marianne is his girlfriend and he says no. Marianne doesn’t tell her friends for a few months either and only admits they are together when pushed by Peggy, but makes out it isn’t serious. Basically they make the same mistake again. Rather than having a conversation and agree to be together, they let the relationship drift along.
At this point too, they are both having a tough time. Connell has lost his job and can’t afford to stay in Dublin. His story has been rejected for publication. It comes out later in the book, but he feels pressure to succeed for his Mum, as she has sacrificed so much for him. Added to this he is surrounded by people with money, talking about their holidays abroad etc. He is feeling anxious, insecure and out of place.
Marianne too has just been back to Sligo and had to deal with her Mum and brother. She is feeling vulnerable, unloved and it has probably dragged up a lot of old memories.
So, Connell waits for her to say that he can stay with her. Marianne just hears that he wants to go back to Sligo. You then have Connell ask are we exclusive (in a very indirect way!). Marianne misinterprets, as it is so hard for her to think she is lovable and assumes he wants to break up.
Neither is in a place where they can support the other. They don’t want to break up, but it has got to the point where there is too much they need to say and it’s just easier.