I'm really surprised by how many people were surprised by the breakup.
As far as I remember, the timeline goes thusly: Dora and Marten hook up amid angst and doubt, but that angst and doubt is soon somewhat dispelled by NRE and first-stage infatuation.
1. They have their small ridiculous fight that shows Dora's incipient controlling tendencies when she freaks out that Marten got a haircut without her express permission, and also her double-standard for her own behavior:
http://questionablecontent.net/view.php?comic=857http://questionablecontent.net/view.php?comic=858Note that she also refuses to critically consider either the rationality of her position or the existence of said double standard until strongly prompted by an outsider observer (Faye). Note that she then has a brief moment of realization where she worries about sabotaging her relationship with Marten, but this moment soon slips away and things go back to the status quo. But it's only the first offense and not a super major one at that, thus so far, so good, until...
2. They have another fight when Dora flips out on him for not seeing Faye's and Sven's hookup as some kind of plot to hurt the two of them, once again demonstrating irrationality and her extreme insecurities regarding Faye and how she places Marten's relationship to Faye at the center of her own relationship with him.
http://questionablecontent.net/view.php?comic=1097http://questionablecontent.net/view.php?comic=1098She then flips out on him some more for "taking Faye's side." In the aftermath, she is shown as unwilling to actually discuss the root issues of the fight or, once again, critically assess her motivations:
http://questionablecontent.net/view.php?comic=1106Overall, it's a fairly short and momentary blow-up, and quickly enough resolved, but it's beginning to be a pattern of absolutely unprovoked over-reactions from Dora...
3. Annnnnddd, it begins. They have yet another fight due to Dora's inability to control her irrational insecurity, where she sets up a ridiculous test that Marten is bound to fail:
http://questionablecontent.net/view.php?comic=1325http://questionablecontent.net/view.php?comic=1326They make up, but Marten's left feeling uneasy and possibly reevaluating Dora's suitabilty for him:
http://questionablecontent.net/view.php?comic=13284. Dora gets her own hair cut and colored without informing Marten:
http://questionablecontent.net/view.php?comic=1671 Doesn't have much to do with other things, but he is obviously not a huge fan of it, and it certainly calls back to their first fight, and again, the double standards.
5. Comparing his relationship to Faye's blossoming new one with Angus, Marten doesn't seem very happy.
http://questionablecontent.net/view.php?comic=1739(The fact that he felt the need to ask Dora in the first place shows he was looking for some kind of reassurance and did not get it.)
6. The underpants fight happens.
http://questionablecontent.net/view.php?comic=1742http://questionablecontent.net/view.php?comic=1743http://questionablecontent.net/view.php?comic=1744http://questionablecontent.net/view.php?comic=1745And then the current one does. I'm also pretty sure there was at least one more instance of Marten-lying-awake-in-bed-at-night that I missed.