- We never find out what the fourth gem does.
- Wataru's wish at the end. Granted the situation with his parents is beyond his control, and it's somewhat obvious from the start that the problems between them are not something he can, or should fix (and, to This Troper, that his dad loved the other woman all along and should be allowed to pursue happiness with her rather than with Wataru's strongly-implied-to-be-mentally-unstable mother), but... what about Mitsuru? Granted, he's probably happier now, given his motivations, but what about his aunt, having to mourn him? Then again, there's also definitely a good case that Wataru's actual wish was the correct one.
Headscratchers / Brave Story