Audio problem: When Doc and Marty return to the year 1955, you hear the squealing sound of tyres braking heavily, but the DeLorean is flying. (01:02:25)
Audio problem: When the crew are running around the passages, a guy with a beard yells something at Bud, and then uses a fire hydrant to put out a small fire. Funny, it doesn't make a noise.
Audio problem: When Russ jumps from out behind the bush and says, "I say that ant is ours", his mouth doesn't move.
Audio problem: When Bill, Ted and the other historical figures are getting Sigmund Freud into the phone booth, in a shot shown from outside the window looking into the booth, Freud says "What are you doing", but his mouth isn't shown moving along with the line. (00:47:13)
Audio problem: During the fight with the Scoleri Brothers, Egon warns doctor Stantz about the sudden apparition of the ghost coming through the wall. He yells "Behind you, Raaay!", but in the close-up Harold Ramis' mouth is not uttering "Behind you." (00:35:50)
Audio problem: When the Enterprise fire the torpedo, the sound used is the old series sound used when the ship's phasers were fired, not the correct noise for a torpedo firing.