Minor Plot hole: James Franco's one-dimensional animal specialist/love interest only learns about the fact that Caesar’s super-intelligence is due to a scientific experiment five years into her relationship with him. Most of their time spent together seems to involve the monkey in some way and we have to assume she never asked nor suspected that it was peculiar for a scientist to have a baby chimp smarter than the average human teenager. Could it be from an experiment ? Oops. Maybe. Would you like some honey while a spoon-feed you the obvious ?
Minor Plot hole: Being the CEO of Gene-Sys comes with many advantages – and we don't mean flexible work schedule and high bonuses here. This film shows us that when your company produces a terrible danger to society, in this case super-intelligent apes, you have the right and obligation to go in the police's helicopter and direct their operation. Try that in real life.
Minor Plot hole: James Franco's scientist associate gets sick from the new virus used on chimps. He starts to caught blood in his handkerchief and yet decides that visiting the nearest hospital is totally useless. He later gets sicker, tries to go see James Franco at his house instead of calling 911 straight up. He is later found dead in his apartment – convinced through the end that shitting his bowels out of his ass will be resolved after a good night of sleep and a Tylenol.
Plot contrivance: A circus orangutan will master the sign language as good as a genetically enhanced super-intelligent chimp. Circus: 1 , Science: 0.
Plot contrivance: The apes and chimps break out of their prison at night but somehow only get to the city during the day. Since Ceasar made the trip alone from the primate facility to James Franco's house and back during the night, how could those chimps be so slow to reach the forest. Since they were all intelligent at the moment, they knew that moving during the day involved a lot more danger and a reduced probability of success.
Plot contrivance: After incapacitating the two men who were trying to make her leave her cage, Caesar’s mother goes ballistic and attacks every sheet of glass she can find while simultaneously running as far as she can from her baby – the one thing she was trying to protect. Let this be a lesson for all monkey mothers – don't do this, it will make you look inconsistent as a plot device.
Plot contrivance: When the ape crashes into the conference room in the beginning of the movie, a security guard guns her down. Never-mind the fact that about a dozen people were standing just behind his target. Good thing rent-a-cops are crack shots.
Unaddressed Issue: Did the chimps and apes from the zoo get intelligent too? They did not get the virus from the canisters. Does that mean the virus evolved to be airborne? Or did they cut the scene were all the intelligent monkeys spit in the dumb monkeys' mouths to spread the virus?