Clearing a dungeon doesn't work properly

[Vivelin]

When saying "Hey tracker, clear Hyrule Castle" with treasure remaining on the counter, tracker will sometimes say "But there's only X left". It's got something to do with tracking treasure but not clearing locations.

The best solution is probably just writing a specific method to clear dungeons, as it's different from clearing any other location and making that method a lot more convoluted than necessary.