This bug occurs when you obtain a "Level-Specific" Key. The key does not disappear from my inventory when I use it to open a locked door. While the subscreen counter "Level Keys w/magic" indicates that I used the key, when I go to "Link Data" on the Cheats menu, it indicates that I still have the key that I just used. I could give you a video of this bug if you don't understand what I'm saying.
Thanks!