My two:
Very cliché, I played Ocarina of Time a ton as a child, have memories of playing it both on N64 as a wee child and on game cube as a less small child. Never got past water temple even with the game guide.
Yu-Gi-Oh forbidden memories. Played the crap out of that game on play station, constantly playing on free play praying for the cards I would need to get further. I was never able to beat more than 1-2 of the high mages. Watching speed runs on the game it turns out I was never ever going to beat that game as a kid. The final 6 are just disgustingly brutal.
This doesn’t answer quite what you asked, but what comes to mind is The Legend of Zelda: The Adventure Of Link for the NES.
I had a Game Genie as a kid. And for some reason I could not get past the boulder to get out of the first overworld area.
It wasn’t until quite a few years later that I figured out some of the Game Genie codes in the official Game Genie code book could have permanent affects on your save file. I had apparently gotten the hammer (which was what was required to break the boulder), but before breaking the boulder, I used a Game Genie code to swap the Hammer for some other item I wasn’t supposed to get until later in the game. So, I was stuck without the ability to break the boulder.
More to what you were asking, The Adventure Of Lolo was a good example. I was pretty young when I first picked it up. Decided it was too hard, and basically never touched it again until adulthood. In adulthood, I loved it.