Really weird bug here.
Occasionally, after pressing play, Playmaker will actually change the name of a particular global variable (playerGO) to an incorrect one (hitObject). hitObject is the name of a local variable I use in one particular game object to store a collision. I can't see any particular relation between this variable and my playerGO.
Anyway, somehow this change persists after stopping, and most of my prefabs somehow update themselves to reference this new, incorrect variable name. However, some don't, and they reference null.
I've corrected its name in the global variables list a few times, but it keeps changing back on its own.