Window and Sound Sets may become unobtainable, or multiple copies may be found.
Window & Sound Set Bugs
Dropped Sound and Window Sets can become unobtainable, or duplicate copies may be received. In both cases, the wrong variable is checked for flags in the After-battle Module, possibly due to a bad extern in the source code, or lingering object code that should have been rebuilt.
This bug has been reported by a few people. It is generally harder to run afoul of than other bugs with collectibles because Connell (who handles the sound sets) and Tenkou (windows) are not recruited until late in the game. It is also harder to trigger because the conflict is with another variable, rather than within the Sound Set flags. This makes it more likely that the problem will present itself by giving you extra copies, if it presents itself at all.
The fix in both cases is simply to force the After-battle module to check the right set of flags. That would be the same variables that handing in Sets to Connell or Tenkou causes writes to, rather than random data that serves some other purpose.