One that I just noticed while watching is this: pirates don't bleed. They can't be killed or injured with a knife. So how is it that they can shed blood to lift the curse?
This one is pretty glaring.
Most of the rest I can sort of see the logic behind (like why Elizabeth hasn't been cursed for the 8 years she had the gold coin), but that just doesn't make any sense. It's okay, the film is still fabulous.
"If you were waiting for the opportune moment...that was it."