I have a new one...
Deathclaws that come into buildings through windows they will obviously not fit through.
Raider armor svcks and looks really stupid at the same time.
Clothing generally just looks stupid, even military fatigues. (my current favorite clothing is undershirt and jeans)
Can't find enough 5mm ammo to justify carrying a 30 pound weapon (same for fat man)
MY MAIN PEEVE:
Sneaking carefully up to snipe an enemy position, taking careful aim (not VATS), and firing at the perfect moment, only to see the bullet strike a railing or rock that was clearly out of the way! How the hell do I p[ut a rifle barell over the top of a banister, and have the bullet hit the banister?!? Invisible rocks and walls that I can't seem to shoot through, but the enemy has no problem nailing me through them with every shot!