Deliberate mistake: The window blind in Maroon's office changes to a sheet of tambour (as found in roll-top desks) just before Roger crashes through it. This was to ensure his outline remains perfectly in it, otherwise pieces would drop out which are not attached to the strings on either side. (00:23:25)
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)
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.