Near the end of the film when Mae says goodbye to Noa, she is shown to be concealing a revolver behind her back in her right hand. Then Noa offers Caesar's pendant to Mae and she accepts it with both hands extended. The gun has disappeared.
Raka would have needed a larger horse to carry his body weight.
When the bunker floods, the water is above the level of the ocean and somehow draining from a floor above the apes despite their floor not being flooded.