Most of them arent really jarring as you watch are they. Sure sometimes they pop into your head later or while talking about the film, but while youre watching they dont normally register. If you watched all films with that level of scrutiny youd never be able to watch action movies at all.
One thing that always bugs the shit out of me though and it has done since I first saw it is the ending of The Lost World. The T-Rex and the infant are in the hold, yet somehow everybody onboard the ship is torn to shreds. Theres even a severed hand holding onto the wheel in the bridge. Even if the T-Rex had gotten loose and then it went back into the hold and someone closed the doors before they died how the f**k did a massive T-Rex kill people inside the bridge without damaging the structure. Did it lift the roof off carefully, eat the poor sailors inside, put the roof back quietly, sneak back into the hold and sit waiting, pretending everythings fine? haha