It's on all the discs, they just put to much on 1 disc and because Majora's Mask was last it got the bug. The game is very slow at first, you need to wait for it to warm up once you start. If you push it to far to fast then you will have a better chance of it freezing (like if you speed run from room to room really fast then it will freeze). I remember when I was playing the Great Bay Temple, I was speeding through it and I noticed it was going slower, so then when I opened a chest..it froze. I know now to be more careful and the game works just fine. As long as you don't rush through the game on the Collector's Edition you'll be fine.
Also I got it used from Gamestop in one of those yellow cases 3 years ago, so it's not with the disc. I also have the VC version but I prefer the CE version.