Given that my post count is still so low, I wanted to hold off on commenting in a more casual forum, but dammit, this thread called my name!
I've got two that are pretty big on my list:
First, back in Yellow (the first game I owned), I didn't quite get the concept of "save before legendaries." However, if I caught a Pokemon, I saved afterwards. Cue me KO'ing Moltres, then catching an Onix (FINALLY </sarcasm>), and then saving afterwards. About a day later I realized the mistake I'd made.
Then, come Sapphire, I'd developed this really weird rule about not having two Pokemon of the same type on my team, ever, under any circumstances. Also at that young age, as soon as I caught a legendary, it went on my team. The problem was, I'd picked Mudkip as my starter. I wasn't about to give up my buddy Swampert, but I absolutely had to have Kyogre on the team. So, after a solid week of playing and building a team, I restarted my game and picked Treecko, just to avoid the situation all over again. My buddies really let me know the failure of that logic.