Okay, this is my interpretion of the movie. Hope this sounds logical. When Leo went into the the time travel, 2 things happened. 1: the history changes…time got mixed up forth and back 2: that means the apes travelled thru time and back, causing the normal earth and planet apes to be changed. For the horses to be there, general thade travelled back thru time landed on planet of apes and brought along an ark of noah(from earth) after they killed the humans on the oberon (crew distress signal was made before they died), Leo landed after that with his human troops and tried to destroy the apes…but they lost, and Leo escapes. So this explained the horses and different species on the apes plane After that, general ape chased max in pursuit. All these happened AFTER general ape landed on earth the same date as Lincoln and killed him. Along with his troops, they destroy the humans at that time. Now how does genaral ape got his space-craft? He escaped from the craft overthrown the humans and rebuilt the ship movie episode. Therefore the movie you are seeing now is actually a middle part of a series…maybe the fifth episode of a seven part movie. Something like the Star Wars. The back and forth future part can be explained by which events happened a lot of times because of the time travel factor
(ship landed on different location and time multiple times by just one time travel because time is ramdomly targeted) . So the picture which the apes put up on the altar, the one which an ape is in a craft is actually the general ape himself! Its very confusing, but lets take it as the events happened by combining past and future happenings which made all these possible because both general thade and leo travelled back and forth thru time. Of course, all these apes surely come from the very oberon ship. And everything starts from the Big Bang theory… Well, its just my interpretion, up to you guys to comment.
Anyone seen the Limey?
DEA Agent: “There’s just one thing that I don’t understand. The thing I don’t understand is every motherfuckin’ word you’re saying”
That’s sort of how I feel right now. More white space next time, ok? Thanks 
-Outrider
What’s the question here?