So after S2 Frank and Matt have been trying to give each other space (Frank avoiding Matt because Matt might try to stop him, and Matt avoiding Frank so he doesn't accidentally give him any leads and can get as many criminals to the cops as possible). When they do meet, they usually work together successfully, with varying levels of murder but lots of arguing. Still, criminals off the streets one way or another is a win.

But Frank gets a lead on the Blacksmith and is determined to kill him. Matt goes after him to both try to stop him from killing and to make sure Frank doesn't get himself killed too. Unfortunately it goes much like the boat: Frank gets the wrong guy (the drug dealer could be related to the Blacksmith or just a unrelated criminal) and Matt knows it and tries to stop him. Frank doesn't care. Frank wants him dead. Matt, however, is able to evacuate the guy by holding off Frank. When Frank sees him getting away, he goes berserk on Matt.

Just give me Frank going Full Punisher and beating the living shit out of Matt without thinking, and Matt just able to fight back enough to keep Frank from running after the guy. At some point (when Matt's unconscious?) Frank comes back to himself, freaks out about what he's done, and carries Matt back to a safe house to take care of him.