If it doesn't give you the alert that it doesn't work on layers above 0 then it is in fact a bug after all @ZoriaRPG .
edit: I would actually consider this one more of an oversight if anything. I'll give you an example Fairy flags only work on layer 0 if you try to place them other layers you get a warning. If this isn't happening with any flags that only work on layer 0 then that should be addressed.
