Audio problem: In the scene where Valiant is outside and looks over to see the brooms cleaning, notice the bird on the bike coming towards the camera. You hear a bell ringing as he goes by but there is no bell on the bike. (00:09:10)

Continuity mistake: When Eddie pours out his whisky, the way he holds the bottle changes between shots. (01:06:35)
Continuity mistake: When Eddie hears his friend has been laid-off, Delores puts her hand over the glass to remind him he needs to have the money by Friday and she takes her hand off the glass when the camera pans up to her face. When it cuts back to Eddie her hand is still over the glass. (00:12:00)
Audio problem: In the scene where Hoskins and Roger are going into the sceret room Dolores says, "oh swell," but her mouth doesn't move. (00:44:00)
Audio problem: In Valiant' office after Roger reads the letter and Valiant says, "Why didn't you just leave the letter there." Notice Roger standing on the bed, you hear him talking, but his mouth doesn't move. (00:38:45)
Factual error: Eddie Valiant sits in his office looking at the "vacation" pictures also on the roll of film in the camera borrowed from Delores. One of the negatives is crooked in the enlarger and shows 35mm sprocket holes. This was not a 35mm camera. (00:26:55)

Continuity mistake: When the movie starts and Herman is launched outside the park, the rattle balls on the bars disappear. (00:01:25)
Continuity mistake: When Judge Doom is about to dunk the squeaky shoe into the Dip, it seems to stick itself in for him, even though it looks rather scared. (00:33:35)
Continuity mistake: At the very end of the movie, when the cartoon characters start singing "Smile Darn Ya Smile" together, Just before the scene changes, the cartoon background is gone. When the cartoon characters lets Eddie, Roger and Jessica go to Toontown, the background reappears.

Revealing mistake: When Eddie fires his "Toon" revolver at the whisky bottle, you can see what appears to be a white, plastic model in his hands. This obviously would've been used as a reference for the animation to be tracked onto later.
Revealing mistake: During the climax, one of the weasels says "Toon Town's right on the other side of the wall, boss!" If you look, you can see a brick moving completely by itself behind him. It literally just pushes out of the hole in the wall as though it's being pushed from the other side. It seems like the other weasel was supposed to be animated pulling it out, and they somehow forgot to animate that part. (He does reach over and grab it for a split second... but then immediately lets go for some reason).
Factual error: When Eddie throws Roger into the bar's storeroom (after Roger was breaking plates on his head), there's a Lucky Strike ad poster with the slogan "Be Happy, Go Lucky." However, the Be Happy, Go Lucky ad campaign didn't start until after 1948 when BDO took over advertising, and the film is set in 1947.
Revealing mistake: In the Acme warehouse, Roger's shadow disappears a split second before the bricks land on him. (01:21:50)
Continuity mistake: When Roger goes to the Acme warehouse, he brings the gold-plated gun that was in Eddie's car after Eddie took it from RK Maroon. This is a real (not-animated) gun, and when Roger is talking to Benny before going into the warehouse, he's holding a real (non-animated) gun. After Roger bursts through the drain, the gold gun he's holding is animated. (01:21:25)
Revealing mistake: Eddie heads into Toontown with an oversized animated gun. As he lurks into an alley, his gun is a plastic prop. During filming, Hoskins would carry the prop gun and the animated gun would be superimposed over it, but the animation wasn't applied to the gun in the alley. (01:13:50)
Continuity mistake: When we're first introduce to Roger, the table on the left disappears between shots, and the pillow he rests on keeps moving closer to/away from the door randomly. (00:01:00)
Continuity mistake: After unveiling the dip machine, Judge Doom explains its functions while waving his cane in the air. But in the following shot his cane is planted firmly on the floor instead. (01:19:15)
Continuity mistake: When Roger blasts out from beneath the Acme Factory grate, Judge Doom lifts his head twice in successive shots. (01:21:05)
Continuity mistake: As Donald plays both pianos at once, the white piano's lid alternates from being closed to open between shots. (00:16:40)
Continuity mistake: After Eddie kicks out the stool and forces a hard-boiled egg into Angelo's mouth, the eggshell fragments on the bar rearrange themselves into a neat pile. Also, two more eggs appear on the bar, which can be seen after Angelo gets on his feet and turns around. (00:13:40)