Plot hole: The nuclear codes are stolen and the Russian guy holding them was let go by Dom. He would contact his government to let them know and the codes changed. Cypher would also know this so her plan is flawed.
Plot hole: It seems highly unlikely that Lucas would be able to "mess with" Mr. Butler's application for a professorship position, or be able to accomplish what he did in such a short amount time. Off-screen, Lucas went into Mr. Butler's briefcase (foolishly left on his desk in the classroom during lunchtime) and (correctly) assumed Mr. Butler's application was on his laptop. Lucas would have to be able to figure out Mr. Butler's password (something that could take forever), find the right file on his laptop, read or scan the application to determine what he could do to mess it up, write a new answer for "qualities that make me a good teacher", and leave the classroom before anyone saw him. Lucas would also have to assume that Mr. Butler would not notice the change when he printed the application, made a photocopy, and double-checked the application before inserting it in the envelope and mailing it.
Plot hole: Buddy is seen at the end of the movie going on the bus that will be featured in Jeepers Creepers 2. When the students and staff encounter the Creeper why didn't he inform anyone that he had encountered the Creeper earlier? The only person that seemed to know anything was one of the girls having a premonition.
Suggested correction: Buddy is getting on the bus to go to the basketball game. When the second films begins, the kids on the bus are celebrating their victory. Presumable Buddy just stayed in the other town for the night or got another ride home.
Plot hole: The world depicted features magic, an evil overlord who 2,000 years before tried to conquer the world, and several races. Despite these HUGE differences with our world, everything turns out of the same as our world, with nations as they are now, and a casual mention of the Alamo and "Mexicans still getting shit" for it. So our current history has not been altered a single bit by wizards, dragons and super-strong races roaming the Earth. Fine. In this ungodly implausible context, orcs live with humans in cities that mirror ours; humans and elves don't trust them, but still they live in towns with them, they go to schools, run businesses, half of the NFL is formed by orcs. Even the movie Shrek exists! And yet, at the end of the movie Nick Jakoby becomes the first Orkish police officer in the USA! There is just no way a society like this, mirroring closely our own and with orcs that existed as long as humans did, can exist with no orc ever been part of law enforcement.
Plot hole: Eddie's colleagues are getting slaughtered in a shooting where they are badly outnumbered and rushed by the villains, but when he meets the group of armed feds Eddie does not even try to make them provide support or rescue his friends; he right away contacts them to have Jamie reach him, at great risk (which is what gets Mason and Vance shot). Who would ever do that? You reach law enforcement and rather than tell them to save your friends, you call your friends asking them to sortie to join you and the group of trained and armed men who are doing nothing? The whole scene is wrong on multiple levels, including Eddie's late reaction.
Plot hole: Donnie Yen rides away on the bike while XXX is still fighting baddies on foot, and when he grabs a bike he fights some more off with one wheeled acrobatics. So Donnie should have a huge head start, and inside the jungle of the hideout he knows and Xander does not. Still, with no explanation a couple scenes later they are side-to-side, Xander just happens to have miraculously caught up with him. (00:55:30)
Plot hole: Henry gave Principal Wilder reasons he believed Christina was being abused: "Bruises, exhaustion, decreasing school performance." When Susan confronted Glenn near the treehouse, she said, "I know what you've done. Emergency room visits, school absences, bruises..." Neither had any concrete evidence/proof. Emergency room visits should have resulted in detection or suspicion of abuse if that's what doctors or nurses believed, and they are among the mandatory reporters. Maybe Henry was wrong. (00:20:35 - 01:30:30)
Plot hole: When Doc outlines the plan to rob the Perimeter Trust bank in Dunwoody, he says it's "right next to the Buford Highway" which allows for a quick getaway. In reality, Buford Highway is multiple miles away from Dunwoody, with the section of the road the truck chase quickly transitions to being nearly 7 miles away. Similarly, this segment then quickly transitions to the John Lewis Freedom Parkway just east of Interstate 75/85, which is another 4 miles away.
Plot hole: When the kids barricade themselves in the basement, Brent and Kendall try to cut through the door, but Josh fends them off with a pistol he stole from his dad. After that scene, though, the pistol completely disappears from the plot; Brent and Kendall don't consider it when they try to gas the children out, and neither kid appears to have it after they escape into the house.