After the boys rescue Dr Weitzman and Riley is pushing his wheelchair, he has a cast on his left leg. However, when he is helped out of the van at the sanitarium, it has jumped to his right leg.
While visiting home, Henry's daughter is wearing a rainbow heart bracelet in one shot, which disappears in the next.
As the van pulls out of the hospital grounds, no traffic is passing in either direction, and the only traffic control is a small portable STOP sign at the guard's booth. However, when the van enters the public road, it passes a long line of vehicles that have obviously been held up for the film production.
About half way through the movie, the van is towed. During the first three feet of the tow, the rear side door is open. The film switches to another angle, shot with another camera, and the door is closed.
Jack claims that Leviticus 5:14 says: "Call not for a doctor, but an elder of the church," but the actual verse is: "The LORD spoke to Moses." The verse he quotes, or more or less paraphrases is James 5:14, which reads as follows: "Is any sick among you? let him call for the elders of the church; and let them pray over him, anointing him with oil in the name of the Lord."
In one early scene Christopher Lloyd, thinking he's a doctor, walks in on Stephen Furst who's singing the National Anthem while watching the start of a Yankees/Orioles baseball game. The hospital they're in is in New Jersey. Though both the Yankees and Orioles play in the same time zone, the clock on the back wall says 10:30. No games start at that time.
When the Doctor walks Albert (Stephen Furst) to the alley, you can see Stephen stop pretending he needs the toilet a little too early (over Billy's shoulder) before entering the alley.
When Henry goes to his wife's apartment, there's a guy painting one of the big urns on the steps. However, there is no paint on his brush.
In two different scenes in the police station, Captain Lewitt calls Philip Bosco's character Maguire. The character was named O'Malley in the credits.
In the scene when Billy is in the van telling the Wolfen (1981) story, the microphone is visible behind Henry's left arm.