Vic, why would Koba be a suspect when they painted it as a human who had done it? Caesar and Koba had their issues but everyone believed in the "ape don't kill ape" law and a human JUST shot one of them in the woods.. It wasn't far fetched to believe it was an assassination attempt put forth by humans.
In a movie where a flu has wiped out 90% of humanity and granted apes human intelligence we are worried that they may not have had proper weapons training.