That sounds a bit complicated. I may also read this wrongly but it almost sounds like you try to create a prefab at runtime. Odd.
Are you using an action like "Create Object"? I don't know but maybe your issue occurs because you try to create an object with a FSM that belongs to a prefab and, for some reason, may automatically use the prefab (the owner of the FSM) as the model to follow.
I admit I don't really understand what's going on.