Because Maya saying, "he gave me the ultimatum that I couldn't see Josy ever again", lines up precisely with Josy saying that them having to separate again feels "exactly like it did before summer" because it is literally just like that. Patrick's ultimatum kept them from seeing each other all summer, we know this, meaning they couldn't spend time together. With Josy moving out of the dorm, it therefore feels similiar to this for her because they are again being forced to stay apart even if it's only in terms of them not being able to have time together in a private place.
Patrick's ultimatum was therefore the catalyst for what's happened since because, as Josy pretty much said in Ep 2, "Relationships when you can't be with each other every week suck, by the way". The literal physical distance was hard on them and it exposed them to feeling pressures and tribulations they hadn't exerienced before. They didn't handle these well because, at the end of the day, they're inexperienced teenagers who simply didn't know the best way to handle these issues. All couples need to learn and develop good, open communication skills and also to not let negative things have an adverse effect on them. This is what the deeper issues are, really, and they're correctly identified in their conversation in Ep 11 as being what this whole ordeal has made them realise needs to be worked on and they both earnestly want to do that. They haven't given up on each other yet and they're going to take the time needed to try and rekindle things.