Misc items defined in one content file are not treated as keys if another content file uses them as such
Scenario: Morrowind.esm defines misc item misc_com_basket_01, which is not a key. my_mod.esp adds a door/container to the world locked by that misc item. misc_com_basket_01 is now a key, but being a key is defined by a record's flags and the record is only present in the master file (where it doesn't have these flags on account of not being a key.) This means that the item will work as a key, but won't be detected by Detect Key. It'll also be possible to sell it to merchants (who do not otherwise buy keys.)
Morrowind.exe has the same bug, but it marks the base record as a key once the player encounters a reference locked by it. Meaning that once a locked door/chest is encountered, its key will show up using Detect Key and merchants will no longer buy the key. This flag change isn't stored in the save game, however.