As seen in my test quest...
If you go in a passageway in an NES Dungeon Special Item room, the item is also made available inside the passageway, whether you take the item or not.
NES Dungeon Special Items appear inside passageways
I can confirm this bug.
it's a real old bug that has always happened as far as I know.
I recall that Zelda Challenge: Outlands makes use of this 'bug' in its First Quest...
This also happens if you forget to check "Special Rooms and Guys are in Caves Only" in overworld maps -- the guy on the overworld gives you the item, but then you also find it in the (Keese-filled) cave. -- Pteryx
At one time the message string also played on both screens, I don't know if it's still that way or not since it caused Link to become trapped and I started building around it.
It really should be fixed.
So the 'bug' is that items appear inside passageways, as well as on the top.
The thing is, if this really "always has happened" then this isn't really a Compatability Bug. And, if it really "always has happened", then some quests in the past might have made use of it.
I guess another quest rule is in order?
How, would a quest have made use of it? what point is there in giving a duplicate item?
Maybe it wasn't a duplicate. Maybe the passageway was the only place to get it.