Whenever the 'lightning' effect occurs as the holy blob uses his power, the shadows of both objects and people show up on the 'sky' and background elements revealing them to be back-drops in a studio.
The nighttime scenes at the beach obviously were filmed in daylight with a filter.
When the Brewster family is stopped at the car checkpoint at the start of the movie, the guard marking them off the check-list ticks over an existing tick, presumably from a previous take.
A subliminal message can be seen at approximately 13:31 into the picture where the kids are running out of the cave. It says "USA" and something else. Not sure if it's a true artifact or not; but this movie was produced during the height of the cold war so the USA message kind of fits.