Just found another inconsistency: one of my prefabs, the first to which I added and FSM, has now a child object to it that I never added.
It's named exactly like the prefab, and when I add it to the map, I only see the parent object, the child object only shows up in the project folder, it disappears when the prefab is added to the map.
Note also that I copied the same FSM to other 3 prefabs, modifying it slightly, and the other 3 prefabs do not show the same problem.
This child object is a script: PlayMakerFixedUpdate. Removing the script from the object doesn't remove the child object.