Sometimes in the past, my N64 would delete our files on OoT and MM. And twice, when I was doing something, Link would warp automaticlly and then it would freeze. I'm still scared that that'll happen. Did/does that ever happen to you?
Yes. It deleted my MM file and it has that warping glitch. Thats normal for a 7 year old game on a 12 year old consol. If it bugs you that much I suggest buying the GC version (although I noticed the warp glitch on that too).
The flaws of N64, there are so many.
This is probably just a flaw because of how it is an old system (seriously, you kept it for more than 4 years of course) and how when it was made it was not entirely perfected.
I still think that the N64s controler is the best to come out of Nintendo (not including the Wii), plus I like that only a few games actully require memory cards.