I believe the is a known bug around subtrees and prefabs instantiation, I believe it is fixed in the newer version which is released soon, the fix I think is:

In BTSubTree.cs, completely delete OnAwake which calls the CheckInstance within. Put that CheckInstance() call within OnGraphStarted later on at line #61 like so:

public override void OnGraphStarted(){
if (nestedTree){
CheckInstance();
foreach(Node node in nestedTree.allNodes)
node.OnGraphStarted();
}
}

I had the same issue where logic was fine, I moved to a prefab tree with subtrees and it blew up, but the author was super fast to assist and fix.