So I seem destined to find weird, 2p-only glitches as I go through this game. We finished the regular levels in Stantonsburg just fine with only one seeming bug - if you go to the very topmost screen of the city (the one where you can only reach the bottom quarter of the screen because the wall is blocking off the rest and there's a big open clearing above the wall) the Shadow Man appears and some dialog happens that looks like it was supposed to trigger when you approach this screen from above.
When it came time for the boss battle, however, we ran into several bits of wonkiness. First off, I couldn't really find any dialog pointing me towards the warehouse, so we kinda wandered with no idea where we were going. Secondly, while all the other exits were blocked, we were able to leave to the West past the (now dead) Frozen Grey (those things scare the CRAP out of my after the gauntlet secret level, btw). This resulted in the scene with zombie mom playing out in the near-dark, making it very hard to tell what was going on. We were also able to go to the prison and get the hammer, but couldn't trigger the scene with the kids.
When we finally DID get to the warehouse boss, we ran into another sequence breaker: At one point, my g/f (player 2) fell into a pit; it was one of the last collapses with most of the screen going. Suddenly, she was just gone. She still had health left, but didn't respawn. I can only assume what happened was that she respawned somewhere off the edge of the screen. I chalked it up as a glitch and went to kill myself by jumping into the pit next to the portal... but for some reason, instead of giving a game over, the screen blinked momentarily to the post-boss area and then to Stantonsburg post-boss battle. We had to redo the boss battle (correctly this time) using the portal to get the post-battle rewards.
And a final tidbit: In several places around Stantonsburg the "broken bridge" item is used as decoration. Once you have the hammer, it is possible to "repair" these into bridges, which often looks weird. However, there is a possibly serious glitch: The transition leading from the south of Stantonsburg to the mines entrance is only one square wide, and that square has a broken bridge on it. If you repair this bridge (say, because your g/f is obsessed with hammering everything she can...) the transition stops working, possibly leaving you unable to enter the mines.