There’s a bit difference between the stuff in JCE and having aliens a couple of hours worth of excavation under New Jersey. He films bad scripts, so he makes them all pretty, but they’re still bad scripts.
As a rule? It’s hard to call Jaws, Close Encounters, E.T. and Schindler’s List ‘bad scripts’. But in this case the script is irrelevant. Hitchcock’s ‘Vertigo’ has a script that’s completely implausible - it doesn’t matter.