Well, there are quite a few, but this one in particular occured to me.
In fiction, the heroic warriors are often able to fight off the vile sorcerer's hypnotic magic through force of will, but one thing that can easily lay them low is "cheating", such as using poison.
But in D&D, that is reversed. A 10th level fighter has a Fort save of +12 or more (counting a high Con and a cloak of resistance), but probably a Will save of like +5 (average Wis, the same cloak). So he laughs at most poisons, but will almost certainly fall prey to mind-affecting magic (an equal-level caster will have a DC of 20+ on his highest-level spells).
Now, I see why this is done from a gamist standpoint (the fighter is the one that has to get into melee with things like giant spiders, and thus needs the Fort save), but it still irks me.