Oh wow, thanks for the kind words! I tested around for a bit and you were right: The time bomb (and also the rocket) do sometimes totally screw you over! So I dug up the Unity project and searched through the code (which is a total mess by the way) and finally found the bug.
In the case of time bombs and rockets the game accidentally overwrote some visuals of the chest, which made it impossible to find material mismatches.I patched the game and it should be fixed now.
Thank you so much for the feedback!