Revealing mistake: In the Acme warehouse, Roger's shadow disappears a split second before the bricks land on him. (01:21:50)
Continuity mistake: As Roger and Jessica get tied to the hook, Wheezy and Stupid switch places between shots. (01:22:15)
Continuity mistake: After Greasy starts up the dip machine, the number of ropes tied around Jessica's midsection changes from two to three within a couple of shots. (01:22:30)
Deliberate mistake: Before Eddie turns on the band machine in the factory, we see Smart Guy holding a real gun. Three shots later, when the weasel is backing away in surprise, he is holding a toon gun, which later switches back to a real gun. (01:23:30)
Visible crew/equipment: In one shot where Eddie leaps into a wall of pogo stick boxes at the Acme factory, a springboard used for the stunt is partially visible behind the red banana skin containers. (01:24:35)
Revealing mistake: Just before a conveyor belt drops the vase upon Eddie's head, an overhead shot shows him pointing at Smart Guy, but actually Eddie points much further left in relation to where Smart Guy is standing. (01:25:10)
Continuity mistake: Towards the end where Greasy laughs himself to death behind the dip machine's wheel, from the point at which he falls out until his ghost appears, the driver's side door window cranks itself halfway open. (01:25:30)
Revealing mistake: When Judge Doom has transformed into his toon-self for the first time, he bounces after Eddie with yellow springs on his feet. Between when he takes off and when he lands, they show 4 different shots. In shots 2 and 3, you can see about 6 black suspension wires running into his clothes and carrying him through the air. (01:26:30)
Revealing mistake: When Judge Doom knocks Eddie off the Dip machine, note the Acme Curve Ball boxes in the background that appear to be written backwards, revealing a flipped shot. (01:26:30)
Revealing mistake: When Eddie is using the magnet to pull Judge Doom toward him, you can see the wires attached to Doom's shoulders used to move him. (01:27:05)
Revealing mistake: When Eddy is fighting Judge Doom, Eddy is holding a giant cartoon magnet. He then attracts Judge Doom's sword and when Eddy drops the magnet it is attracted to a steel drum. If you look at the bottom of the drum you can see two strings on the bottom of the drum as it moves towards Bob Hoskins. (01:27:10)
Continuity mistake: After leaving Judge Doom to be flattened by the steamroller, Eddie runs over to the dip machine and turns off the ignition. If you watch as Roger and Jessica are about to be blasted with dip, the stream of dip goes from being on their left side, to right, then back to left again between shots. (01:28:35)
Revealing mistake: After being flattened by the steamroller, Judge Doom staggers over to the compressed air tank and reinflates himself. When his black hat pops off, strings can be seen pulling it up. (01:29:45)
Revealing mistake: When Judge Doom gets sprayed by the Dip spraying machine, stunt cables attached to him are visible, pulling him backwards. Christopher Lloyd also seems to have been replaced with a dummy. (01:31:22)
Audio problem: After Judge Doom gets sprayed by the Dip spraying machine, he stands up and says, "Oh no!" but his mouth stays shut. (01:31:47)
Continuity mistake: When Judge Doom is melting and is just about to die, the wide angle shows he's surround by a very thick cloud of yellow smoke that keeps us from seeing his face, then in the close-up it changes to a very thin smoke that allows to see his face, and then back to the wide angle and the thick smoke again. (01:31:55)
Continuity mistake: When the spray-machine is about to kill Roger and Jessica it smashes a brick wall with some lettering and a thick white line painted below. In the close-up the lettering and the line are gone. (01:32:25)
Continuity mistake: After saving Toon Town from Judge Doom, Eddie lowers the giant hook and starts untying Jessica and Roger. He throws one rope offscreen and the other just slips from the hook on its own. But in the following shot no rope can be seen on the ground directly below the hook where it should have landed. (01:33:10)
Continuity mistake: When Roger starts reading Marvin Acme's will out loud, Jessica takes her left hand and rubs his head, but once the shot changes her hand is nowhere to be seen. (01:35:05)
Revealing mistake: After Roger reads Marvin Acme's will out loud, all of the toons start jumping for joy. Meanwhile the music machine is still activated in the background, and its colorful flashing lights are being reflected on the ground near Betty Boop and Tweety at the front of the crowd. With all of the toons grouped together like they are, the machine's colorful lights should have been obscured, not reflected. (01:35:30)
Answer: There's really a lot of possible reasons he hates other toons. There's a whole Roger Rabbit book and comic book series that explain Doom's background more. In the film, he's greedy and wants to destroy Toon Town to build the freeway to make more money. In human disguise he's also seen as merciless and is just punishing toons to maintain law and order, etc. Although that's just an excuse to kill toons as well. However, not explained in the film; as a toon he was cast as the antagonist in cartoon films until an accident one day left him thinking he was an actual villain (as opposed to just an actor playing one). That's when he began his life of crime, including killing Teddy Valiant. So his hatred of toons is more about him being evil and not a personal vendetta against them, like Blade's motives.