I... did in B/W when I realised I shouldn't EV train Litwick in attack because I thought special attack only applied to super effective attacks. :( /sodumb
Hmmm what else...
I hadn't explored all of Castelia until MONTHS after playing it and wondered why everyone talked about a certain location and couldn't find it - it was in that end street which doesn't look like there's buildings there! I'm sure I've done other dumb things, imma try to recall.
Also I'm just going to specify that this is for Black and White in the title because otherwise people might end up posting about other games.