These have been hotfixed since the middle of last year.
The only gamebreaking bug is a save bug in a specific room. You'll know the room, because it doesn't allow you to save it in, working around the issue entirely.
The stylus and the dual screens are an absolute godsend and make the game much much more enjoyable to play. Due to the nature of the gameplay you WILL find yourself getting annoyed by only having 1 screen.
The only advantage to playing it on the Vita is the graphics are better, but the environments and models are so fucking terrible it's arguably better looking on the 3ds because you have a harder time telling what you're looking at due to the smaller resolution.