I bought a copy of the LE from amazon. Figured I'd look for these bugs and report my findings. I tested these parts of the game on both my 3ds and my friend's 3ds XL.
In the main game, Zels3013 mentioned it crashed at Saito's part in chapter 3. I played the game to this point (without skipping text) and didn't have any problems. No crash on either of my systems. It has to load a special effect here so maybe that is contributing to the crash Zels had.
I played through Memories Mode for Hijikata, Okita, and Saito, so far. Several times I tried it on my regular 3ds and no crash. On the XL it did crash the first time playing Okita, at the same part as everyone else- "Rephrasing's not going to help." On the second try I hit the Auto text button, and no crash. Third time I tapped the A button like normal, no crash.
Perhaps some copies are more defective than others? Or perhaps the amount of data and system updates on everyone's systems affects the likelyhood of a crash? My regular 3ds doesn't have the most recent update yet, but the XL is completely up to date.