I'm currently on 1.8.9 and Unity 2017.3.0f3 and having this issue - indeed it might be something from copying variables/actions with those variables into another FSM. Haven't been able to reliably reproduce it yet though. But I've had this issue since maybe 1.8.5? Around the update that brought in categories.
Also worth noting that a byproduct of this is when you create a new variable of that type, it will sometimes shift ALL your variables values of that type up if that makes sense.
example:
Bool1 - false
Bool2 -
trueBool3 - false
Create new variable called Bool0 and this happens
Bool0 - false
Bool1 -
trueBool2 - false
Bool3 - false
Super annoying, makes me perpetually scared to create variables for fear of having to go through my prefabs and re-set them again xD
Deleting all the variables, then remaking them doesnt solve this either. Neither does reverting the prefab (I had thought at first it was an prefab-edit slip).
Would love to figure out a course of action for this please
best,
craigz