This is a followup to Doug Cole's post on the subject of GURPS Rules you've run incorrectly.
Here are a couple that I ran wrong accidentally:
Eyes Give 2 Ablative DR - Eyes are crippled on injury to them exceeding HP/10. In 3e, it was a flat 2 HP. We ran it that damage to the eye had to get past these 2 HP before doing any multiple for the Brain (3e) / Skull (4e) hit location.
The problem is, that's not what the rules say. You don't have to cripple the eye to inflict damage to the brain. It says clearly, that injury over HP/10 blinds the eye . . . and "Otherwise, treat as skull, without the extra DR!" (The skull has 2 DR.)
So we'd, say, have a victim shot in the eye with an arrow for 3 HP of damage, knock off 2 HP to "cripple the eye" and then have 1 HP of damage get the x4 injury multiplier and do 4 HP of injury. Total injury - 4 HP and you're blinded in one eye. But "treat as skull" means you just get that x4 multiplier on the damage . . . and if this exceeds HP/10, the eye is blinded. So this 3 HP of damage becomes 12 HP of injury, and the eye is crippled along the way.
Conscious Checks Immediately - this one we did for a long time, in fact until recently. If you suffered enough injury to potentially lose consciousness, we'd roll that immediately. Actually, you roll that on your turn, not on the turn of the person inflicting the injury.
Because of this, torso shots for high-damage fighters was the way to go. You didn't want to waste any damage and it was often instantly incapacitating. You could knock a foe down and out and know right away you'd done enough - no one else would waste attacks on that foe.
Changing it back to the rules as written and intended had an interesting effect. You are better off aiming for a hit location that comes with a high chance for knockdown and stunning, since that could knock a foe down or even out cold - both immediately.
Those are two that come to me off-hand. I know for certain I did others wrong, either accidentally or as house rules.