This is in build 1281.
Here's the problem: whenever I get a key, bombs, or a blue rupee in this quest (it could be other items, too. These are the only ones that have reappeared on me.) and collect them, if I exit and reenter the room, the item reappears. Here's the quest that it's happening in, and here's a video of the glitch. The example I showed in the video is on Map 2, Screen 01, and it's also happened with a key on Map 2, Screen 6B. I can't think of the locations with the bombs and the blue rupee right now.