I think that ultimately the bottom line here is that this is mostly a matter of miscommunication. I say "mostly" because yes, there are other factors at work here, but I think miscommunication is the most prevalent. Most of this stems from Dora's insecurity, but that isn't to say that Marten doesn't have a hand in it as well, no matter how small.
Let's look at the facts here: First off, and perhaps most important, Dora is extremely insecure and is more prone to being irrational than the other characters in the comic. Case in point: the underwear incident and the haircut incident, both of which lasted for several strips before they were resolved. They were ultimately minor issues that should not have been problems to begin with, and yet they became a huge deal when Dora flew off the handle. But looking at Dora's track record with her previous boyfriends it isn't hard to see why this might be the case. If all of her previous S.O.'s were really as horrible as she and Sven have made them out to be, maybe she's just inadvertently worried that Marten will fall into the same stock. Despite evidence to the contrary, she's worried that he's just another asshole who will walk over her, so minor offenses erupt into huge confrontations.
Now, that said, this particular issue could have been avoided relatively quickly as soon as Dora followed Marten into his room to try to "apologize" (because let's face it here, based on her wording and body language, Dora's apology was most definitely NOT sincere). Marten obviously left the room because he needed time to cool down before talking to Dora. And what does Dora do? Back him into a corner, literally. Instead of telling Dora "I'm not ready to talk about this right now, I need some time to cool off," he immediately attacked her. That isn't to say that it wasn't necessarily unwarranted, but it wasn't the right time to be coming forward with the stuff that he said. Granted, he was angry and probably wasn't in the best of mindsets at that particular moment. But even so, simply telling Dora to back off until he calmed down could have easily avoided what has come to happen now.
Dora's got issues, we can't deny that. But both parties need to be willing to work through rough patches in any relationship, and this is certainly no exception. Dora and Marten need to sit down and have a nice long chat if they have any hope of fixing this mess.