I've noticed this happens to me almost 90% of the time I'm in south east Hyrule Field, near the trees. I'm not sure why it's happening, but it seems like when the poe appears, it fixes it for a certain amount of time. The following things have happened while experiencing this glitch.
Softlocked game with a weird frozen link (from trying to take out chus)
Softlocked game trying to play the ocarina (if the animation from the song is missing, happens mostly with the Sun's Song)
Softlocked game with Link stuck in place trying to take out the hookshot (sometimes he runs forever in place, sometimes he actually get somewhere)
Also, this may sound really strange, but the game actually saved on its own. I started up with chus on C left, hookshot C down, and bombs on C right. I replaced C left with ocarina and caused a Sun's Song softlock, and when I booted back up the ocarina was on C left. (edit: I used crooked cart to see what it would do to the softlock, maybe that's somehow related?)
Trees sometimes disappear, and grass can disappear/reappear. Sometimes if an item doesn't work, you can equip it to a different slot and it will.
Basically I just felt like sharing some things about this glitch. It's very interesting and I wish I knew more about how it worked.
It seems to happen extremely often for me, is this more common on N64?
Yeah this is known to happen mostly in that area of Hyrule Field because of all the trees and bushes concentrated there. When there are too many objects loaded, the game refused to load more. This includes items Link would normally hold in his hand, which can screw up some of the animations, softlocking the game. Here's another video with an example of a softlock
http://www.youtube.com/watch?v=DmIu67lImNU
