Back in Pokemon Red I didn't know I was suppose to go get Flash, so I couldn't figure out how to get through Dark Cave. By the time I figured it out, my main was at level 50.
On the same game, because I started watching the anime first, the episode where Ash's Charmander easily defeated Golem gave me the impression that Rock-types were weak against fire. I found out the hard way when I faced Brock.
In Gold I was trying to capture Entei. I was on Route 38 when I ran into him. He fled the battle, and I went a little ways further. I wasn't paying attention, I mistook a Tauros for Entei, and through my masterball. I didn't realize it until I had already saved.