What do you mean by mutated and deformed? Do you mean that if the apes have evolved from their primitive form then why haven't the humans evolved (or devolved) themselves?
Firstly, we have to consider that only about 3,000 years have passed, which isn't a lot of time for dramatic changes in natural evolution, particularly when considering generations that are separated by decades. However, the apes when they were on the ship were genetically enhanced to begin with, so maybe that aided their own evolution to some degree, accelerating it. Yeah, a stretch, but it's an answer of sorts. Another argument is that the apes look fairly human-like to the viewer, but to the characters on the screen, they look like current apes. I don't follow that line, but it is an argument to consider and solves a few problems (bar Pericles not being like them).
As for horses... forget the horses. ;) Well, I suppose it could be argued that the Oberon had a horse department that wasn't shown (I mean, the Oberon must have had toilets, but you never saw them... I know ;) ). Still, that's a stretch too far to be believed. One of the books that were based on this film's story dealt with the time when the Oberon crashed onto the planet. For a short time, they conveniently had some genetic manipulation machines that could create all sorts of things, horses being one of them. Still, a big and convenient stretch was needed. All in all, the horses can't really be explained while keeping a straight face, and, unfortunately, have to be considered a "the wizard did it" type of thing.
So, no, you didn't miss anything. The planet that Leo arrives on with Ari and chums is another planet. There were no humans on that planet prior to the Oberon crashing on it. Humans became primitive, but they didn't devolve into animals (a pity that they didn't, but Fox overruled Burton's intent that the humans should be mute). The apes over 3,000 years evolved and created their own civilisation. Horses are a mystery (Semos did it...). When Leo leaves the planet he flies back to Earth to find that there's an ape welcoming party. Surprise!
In the end of the day, a lot of stretching of reality and short cuts are involved in making a lot of these films. Many would say that this film stretched too far. A horse too far...
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