When Miles is carrying the sleeping Becky from her house to his car, her right arm is hanging limp on the way down the stairs and her left arm is holding Miles. But in the next shot at the front door her body position is changed, with her right arm around Miles shoulder and left arm hanging limp.
Near the end of the movie, a character falls asleep for an instant and wakes up as a "pod person." This contradicts the entire premise of the rest of the movie, in which humans are physically being replaced by "pod person" duplicates.
As the posse runs through Bronson Cave, after the policeman stops on the planks, says his lines, and then runs ahead, look closely for the man in the white shirt: it looks like he fell down onto the planks before the shot ended.
Upon discovering two pods in the trunk of his car after visiting the gas station, the hero pulls them from the trunk and sets them on fire with a highway flare whereupon they burst into flame. Nowhere else in the film is there any suggestion that these pods are flammable nor would they be if germinating into a human replica.