Plot hole: Spoilers. It's revealed that the barn game takes place at an old farmhouse owned by the family of Jill Tuck - Jigsaw's widow. It's public knowledge that she was married to Jigsaw and that buildings they owned served as the headquarters of several past traps, so the barn should have been investigated at some point in the meantime. Ten years have passed. It makes no sense that the barn was never investigated and that the bodies of the barn victims were never discovered.
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.
Plot hole: This movie introduces, rather casually, nightshade as a vampire vulnerability. It works practically as in the videogame Skyrim, so whoever wrote it in the script most definitely played it. The problem of course is that a toxin that can murder most vampires and indefinitely paralyze the strongest elders, is a world-breaking concept that would have ended the war hundreds of years earlier, and instead is never used before or since the small scene it's instrumental to. Foreign translations which identify the nightshade with the more specific Belladonna plant (one of the most commonly used herbs since the ancient times) further aggravate the problem.
Plot hole: There's no way that plane could have crashed and stayed intact like it did.
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.