Koba tells Blue Eyes that his scars make him strong. Koba received his from abusive humans, which resulted in his intense hatred for them. This is a clever foreshadowing of Koba's (initial) influence on Blue Eyes's opinion of humans.
Given how it's pointed out from the beginning that human civilization crumbled in the 10 years leading up to the film, it might seem like a coincidence that Dreyfus managed to contact a military base for reinforcements rather than, say, another survivor group. That is until one realizes that the C.D.C. in real life (and the U.S. Government in general) is known for anticipating potential dangers to the point of being Crazy-Prepared, including a zombie apocalypse.Coupled with Dreyfus having a military background, it wouldn't be surprising if there were at least a couple of safe zones and military facilities still functional out there.
As well as the fact that, in such an event, many survivors would be likely to flock to a military base; It's a sturdy shelter, with weapons, supplies, and (most likely) authority figures. The military might even be recruiting survivors to keep numbers up.
Doubles as Fridge Heartwarming: Why was Caesar's second son with his father and brother, instead of his mother? Because, as we discover later, Cornelia was very sick. Caesar wanted to let his wife rest a bit and decided watch to over their baby son.
Also, baby chimps are not as dependent on their mothers as humans are; they're born with significantly better motor skills than we are, and develop significantly faster.
Everybody was surprised when they saw that the apes could talk. Most of the audience must have thought: they should have known, it happened in the previous film. But... should they? Apes did not talk during the big fight in the bridge, and only one person heard Caesar's words in the woods. There's Caesar's Big "NO!", which is recorded, but it may not be enough to start a big social or scientific commotion just yet. People could have thought that it could have been a noise that sounded like a "No", a sound learned by imitation... or, more simply, just a scam video. Who would have taken seriously a video with an ape talking? Plus, the Simian Flu must have been distracting everybody away from such mundane concerns.
Caesar declaring Koba to not be an Ape wasn't a No True Scotsman argument, at least not entirely. Koba cited that Ape shall not kill Ape; but following that logic, Koba (having murdered Ash and knowingly attempted to kill Caesar) no longer counted as an Ape. Granted, he was entirely willing to overlook that contradiction, but it meant all Caesar was doing was holding Koba to his own words.
Koba's last words are another Fridge Brilliance. Caesar's main teaching is that Ape Shall Never Kill Ape, which Koba considers to be weak. If Caesar helps Koba up, Koba will simply kill him. If he lets Koba drop, he will violate all of his teachings. Either way, Koba wins. If he lives, he can just take leadership of the apes again. If he dies, it will mean Caesar will have to live with the fact he violated his main commandment.
Ash's death was actually foreshadowed. First, he was in shot close ranged by Carver. Then, he was brutally murdered by Koba. Both Carver and Koba are human and ape counterparts to each other.
Koba's Last Word (a Big "NO!") make him an even more perfect Foil to Caesar than previously thought. Caesar's first spoken word is also "No", which he spoke to courageously defy Dodge Landon of the first film and launch the apes' breakout from the sanctuary. Koba screamed out his last word of "No" as a selfish, cowardly reaction to his realization that he was going to die. Before that, he had never once used "No" to demonstrate his courage and his compassion for the other apes.
When watching the film alone, Koba pulling off a convincing performance as a dumb ape when interacting with the two guards at the armory may seem a little silly and somewhat out-of-character. After reading tie-in materials that explained Koba was born and grew up in a circus before being transferred to Gen-sys, it makes perfect sense.