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.
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.
Plot hole: Considering how important it is to the Analyst that Neo stay connected to the Matrix at all times, it is unfathomable that his body in the real world is unguarded. While keeping an eye on him inside the Matrix at all times is difficult, there is no reason whatsoever that he should be left alone inside his pod with no security for even a second. This is an entirely different scenario than the original 3 films where resistance fighters finding Neo was integral to the machine's plans.
Plot hole: Dan returns from the future with a vial of toxins with him that can kill all the white spikes. He tells somebody to start mass-producing it but this information is not spread across governments or even made public, but it is the one thing they have that can prevent humanity's extinction and making people aware of that will stop the rioting.
Plot hole: WW mentions that "As Darkseid waged war on Earth, he found a secret there", that being the Anti-life equation. But later on it turns out that after being defeated, planet Earth is so "anonymous among a trillion worlds" that he never manages to find it again and destroys another 100,000 worlds (his words!) to look for it again. That would mean that they lack any sort of navigation, and it's hardly possible anyway that the planet would be "anonymous" when it contains what Darkseid wants the most.
Plot hole: Kyle got a flat tire and there was no cell phone reception to call for help, so he and Julia decided to walk to the Ghost Town. However, almost all vehicles - especially a relatively new SUV like Kyle's - have a spare tire. Kyle surely had a spare and could have at least tried to change the tire himself. (When Kyle saw his damaged tire, he complained that it was a $300 loss, not that he did not have a spare tire with him). (00:04:55)
Plot hole: Blind Master can sense when a person is lying. When Snake Eyes admits he is not pure of heart he explains this is because he is driven by his desire for revenge on his father's killer, which Blind Master reads as a truth. However, this is still a lie: a lie of omission. Snake Eyes is only telling part of the truth and omits the fact he is betraying the clan on Kenta's behalf to get his revenge. Snake Eyes is being deliberately deceptive, which is the definition of lying.