Way back in Generation I, I was convinced that there was a set hierarchy of priority moves. Quick Attack was obviously the fastest move, but in my mind, Swift was the next fastest, and so on and so forth. It took me a while before I realized that the priority was based on the Speed of the Pokémon involved, not on the moves (with the exception of Quick Attack).
Aside from that, most of my mistakes came from cross-generational changes. I remember being confused when Poison and Bug were no longer super-effective against one another, as well as when Magnemite suddenly resisted all sorts of stuff it never had before. I also got hit when certain Pokémon became immune to Earthquake via Levitate, as many have said.
