I didn't post this at first as somebody I bumped into on multiplayer said that the glitch was known and would probably be fixed in the next update, but seeing as that next update came around a while back, I can only assume the devs weren't actually familiar with this issue.

The issue is that the mission editor is just broken in the sewers. When you start up the mission editor, the box appears on the ground but the editor menu doesn't open up until you close the pause menu, and when you try to start mission, it will just say that the mission has been saved and not start the mission.