I found another stage-related glitch in SSB4 for the 3DS.
1. Go to the Gerudo Valley stage in a mode where you can pause and move the camera (pretty much anywhere but Training)
2. Pause.
3. If you see the large hole at the top-left corner of the stage, then zoom in, rotate, and pan the camera so you can see inside of it to the left. You should be able to see a black hole. This seems to be easier on the Final Destination version of the stage.
Also, I checked, and this does work on version 1.0.4.