Aliens
After the first big fight, the aliens have to crawl through the ventilation shafts to infiltrate the colonoy HQ. Can't they just bash the doors down? Wouldn't that be quicker, anyway?
E.T.
It's pretty convenient that ET and Elliott can fly across the sky to evade ET's capture, so why didn't they do that sooner? They really needed that at the beginning with the government agents hot on their tail. Kind of weird how they only used this device once.