Having not played the game, it wasn't apparent to me. And once again, so what? Explain to me how this matter in the slightest? Miss placed video, wow.
I decided to watch the video again, and now that you pointed it out, yes I noticed it, but having not played the game, it wasn't noticeable at all. Maybe it was the crappy camera work, maybe it was because I haven't played the game, but it's not really noticeable unless you know what you are looking at. He might of explained it in his video, but who listens?
Screen is stored in a memory location. For whatever reason, which HOME is hit, the starting point of the redrawing the screen isn't getting set back to the top of the screen, it's going to a different location. Since there are no garbled graphics on the screen, it most likely not overwriting any memory, or grabbing other parts of memory, it's showing what is there, it just starts the drawing at the wrong location.
Since I am not a 3DS developer, I do not know how the swapping to HOME works, so I can't say for sure where the error lies, but since it only happens on this one game (apparently), it's probably some minor error that a compiler doesn't catch.
But as I said, not useable to hack the system generally.