I've actually seen this bug since 357, but haven't bothered to report it until now...
Apparently, if you disable some items on a DMap, have those items, and pick up a new item on that same DMap, you'll be able to use the Disabled items despite them being...well... Disabled. An example quest is actually my latest Realm of Mirrors demo, which is here.
To recreate the bug in that quest.... Go get the sword from the Mysterious Tower (or use the Level 4 cheat of test), then go into the shop in Arboria Village. Buy ANYTHING inside by pressing A when below it, and you'll see Link slash. He's not supposed to do that. If you try to use the Sword before buying an item, nothing should happen. Now, you could say that's because of my script. But try it out on a new quest, except with a normal screen item instead of a script giving one. It WILL happen again. Of course, in 726, it'd be difficult to do in my quest, due to Disable flags apparently removing the items from the inventory until you use my Shop script. O_o (Seriously, what's up with THAT?)