Continuity mistake: In one scene after Hutch is beaten up on the bus, he has no facial injuries. Then in the next scene, they are back.
Plot hole: The whole premise of the movie is that due to a botched spell, people who happen to know that "Peter Parker is Spider-Man" are pulled inside this universe. It's a bit of a stretch already that amongst those people is...Peter Parker himself, twice over, but let's say it makes sense. The problem is that Jamie Foxx's Electro does not meet this condition; he never found out. You could say it's a retcon or it's a different universe from the original movie's, but even this cop-out explanation is negated by the movie itself when Max Dillon makes a joke that shows that he didn't know Spidey's identity or even race.
Factual error: The sisters run out of fuel for the helicopter, which is then shown slamming down on the ground and essentially destroying itself. All helicopters are capable of autorotating safely to the ground in the event the engine(s) quit. Of course, that would not have been as dramatic. (01:05:15)
Factual error: Although it's a commonly used movie trope, cutting the brake lines on a bus would not produce the effect seen in the movie. Buses use air brakes, which by design, can operate even with substantial loss of pressure and often engage automatically if there is too much pressure loss.
Other mistake: After realising they can track the mother box, Batman says they have to go back to his base to use one of his satellites to track it, and they all do so. Which completely ignores the fact that Cyborg could easily access the satellite feed directly using his abilities and display it to the others on any nearby screen in Star Labs.
Factual error: Druig leads several warriors outside Tenochtitlan as it was sacked by the Spanish conquistadores, and they live peacefully in the nearby forest, for 500 years. The forest is of course the virgin Amazon forest, as captions say. Small problem; Tenochtitlan was in Central Mexico.
Factual error: Let's go by the movie geography; our planet is a big matrioska. By diagrams shown, this Hollow Earth would be by the Earth's core, thousands of miles deep. They enter from a portal in Antarctica. And yet, Godzilla later in the movie burns a random hole in the ground in HK deep enough to reach it, roars through it and Kong hears it, and the ape easily climbs it to poke back to the surface. Even admitting you can do the magic "1,000 miles in 2 seconds" warp anywhere, the scale is ludicrous.
Other mistake: On the prison computer scan of Ernst Stavro Blofeld, Blofeld's date of birth is shown as 4th July 1946, but he is only meant to be a few years older than James Bond, as seen in the photo of them together as teenagers in the film Spectre. That photo is meant to be circa 1985, and the newspaper clipping (also shown in Spectre) about Franz Oberhauser's (aka Blofeld) death in the avalanche happened when he was 16 years old. If he was 16 in 1985 then he should have been born in 1969, not 1946.
Plot hole: A core plot point (lifted by the comics) is that Venom needs phenethylamine, and the only way to get it is from brains and from chocolate. Let's just go with it and forget the fact that phenethylamine can be legally purchased as dietary supplement, which would solve every problem. So, Venom gets incredibly angry because Mrs. Chen's shop ran out of chocolates, and *therefore* they need to go raid a chicken plant to eat some chicken brain. Uh, Venom lives in San Francisco. Chocolate is sold everywhere. If Mrs. Chen ran out of it, there are hundreds of stores and vending machines that have it in abundance. The escalation does not make sense.
Factual error: It is not possible to have a conjoined twin of the opposite sex. They are similar to identical twins, which are always of the same sex, in that they are formed from a single zygote. In the case of conjoined twins, the zygote fails to divide normally.
Factual error: The morning after the ambush, Cyrano meets with the baker asking for a private spot. Ragueneau is an amateur poet, and he reads his composition. When Cyrano asks for a place more private than the oven surrounded by men, the baker recites "Jupiter and Pluto are planets, revolving like us, far apart." The story is set in the 1600s, and Pluto hadn't yet been identified as a planet nor sighted, let alone named. It happened in 1930. (00:28:40)
Plot hole: Johnny's dad jumps in his truck and gets to Johnny in moments. That same journey was shown to be an overnight bus journey for everyone else.
Factual error: Lt. Harp is told by Capt. Leo that the Lieutenant has 56,000h of UAV flying time, That is ridiculous. Even seasoned pilots of the Military Airlift Command do not have that many hours. Drone pilots can fly up to 1,800 hours a year, and Harp hasn't been flying drones for 31 years straight.