-Just when you have a good set up.....critical hit! Strategy is ruined. Also the bane of nuzlockes. 
-HMs....I think this doesn't really need much of an explanation. 
-NPCs that use Kingdra (even though I like Kingdra). Screw Clair and Juan.....especially Juan. 
-Facing Lissia in a pokemon contest. I was already annoyed with doing the contests anyway....better make it tougher. I just wanted the lucarionite. 
-Frozen status 
-Double Team/Minimize 
-Wobuffet. Only choice is to attack it, but you better hope you one shot it or it uses the wrong move, because you're gonna lose a mon to it. Only chance of running from it is if you sent out a ghost type first. 
-NPCs that use Crobats and Golbats. Getting real tired of supersonic/confuse ray. 
-You use a move that has less than 100 accuracy and miss a lot, while the opponent uses the same move, but rarely misses. 
-Last but not least, roaming legendary pokemon. Worst one for me was Thundurus. It was down to 1 HP and paralyzed for 6 or so months and it just wouldn't go into the ball.