Hi!
The 3D is obviously ghosting.
Caused by the upper screen unfortunately. It's either the screen it self or the ribbon cable.
Replacing the upper screen is probably the only way to fix this...
I'm not gonna lie, it's very hard to fix this, but worth it!
Guide: [guide|6176|Nintendo 3DS Upper LCD Replacement - iFixit Repair Guide|new_window=true]
If you have any more questions, please let us know!