When playing The Guardian Legend as a kid, once I got to the hub area (assuming if I got to the hub area), I would always wander around aimlessly having no idea what to do and no idea how to go through the sealed gates. Years later I realized that the game puts markers on the pause screen’s map, and I was able to finish the game in a week.
Playing Mario & Luigi: Superstar Saga, I never really used the team attacks during the first half of the game, because I didn’t like memorizing the button sequences and because the damage output seemed low. Later in the game, I somehow realized that the team attacks levelled-up as you used them, and that they were probably intended to be your main source of damage. That moment was the first time I had an intelligent epiphany about an RPG system, but it also marked the moment when I dropped the game, because I didn’t want to grind the team attacks to bring them up to speed.
I also had a similar experience with Majora’s Mask and the Bomber’s Notebook as a kid (when I was about 10 or 11, IIRC). I was able to get past the initial three days, but after that I didn’t want to interact with the bomber kids at all because I was somehow projecting my shyness/social awkardness into the digital realm. IIRC, this meant I didn’t get the Bomber’s Notebook, which meant that I could progress in the game, but I was missing out on the lion’s share of the game’s interesting content. (I had a much better runthrough of the game several years later that petered out around the stone tower temple for reasons I can’t remember.)