I am not sure if this is a bug, but I do not believe it should be intended behavior.
In Rumble Run when you use your shrine to attack and the Hunter Secret to “shuffle attacking card into deck” is activated it will shuffle your shrine into your deck instead of making it inactive for three turns.
My understanding is the shrine that you start with will not leave the board under any circumstance and will only be inactive for 3 turns. This may just be my understanding, but it was something that made a level really hard to beat without your shrine.