I do know that Majora's Mask on the GCN freezes often, I have it. There are also some other glitches, mainly a lot of lagging (mostly in Clock Town, though). Also, it's common to hear choppy sound while walking through a door if the music doesn't stop while going through. This is because the game uses a lot of RAM and it is emulated instead of being a direct port. Although, it has been confirmed that the game freezes less if you have the Rumble Feature turned off. I played through it again recently while doing this and it helped a lot.
The VC version, I've heard mixed things about it. Some say it does freeze like the other one, others say the problems are not present on it. Although Clock Town lags a lot on the GCN version, and if it doesn't lag on the VC version, then it probably won't freeze a lot.