I've had this happen too, today it was pretty bad :/
I changed an action which was referencing a global variable, and it made the same change on other FSMs on the prefab, breaking a bunch of stuff
I've had it happen before but I was always not 100% sure what happened, but this time it was just too obvious. I'm guessing it does have to do with applying changes on prefabs, but since you only have access to the first level of children on the hierarchy, you kinda have to do it sometimes, it really shouldn't break everything