Plot hole: They aren't able to travel before the birth of their children or their children become different. Despite that, he visits his father one last time before their third child is born. His Dad and he then travel back to when he was a kid, which would have changed his first 2 kids.
Suggested correction: This is not necessarily inconsistent with the movie's time travel logic. Since Tim goes back in time to visit his father and inside that particular time travel, they use time travel to go back to a day where Tim was a child. Then, they return back to the original time travel where they're playing ping pong. At that moment, both of Tim's kids were already born. So, when he returns from the ping pong scene, there's no change regarding his kids.
Also, paraphrasing the Dad, he said they aren't going to change anything. It is more like reliving a memory than changing the future to get what you want. The Dad couldn't go back to not smoke before his kids were born because that was major and would have changed the course of his life; walking a bit differently on a secluded beach that you walked on in your younger days (as long as you spent the same amount of time - presumably) would not alter the trajectory of one's life.
The slightest change in 1 second of being on the beach would absolutely affect his kids. A man produces 1500 new sperm every minute. Altering the timeline and delaying every event that is going to happen by literally 1 second would most definitely alter which exact sperm was used when conceiving both of his first two children.
Plot hole: When Jake first meets Reggie, he tells Reggie that the Great Turkey told him everything about him. Later in the movie, when Reggie goes back in time and introduces himself as the Great Turkey to a young Jake, he only tells Jake to find the "Pardoned Turkey" but never said that the pardoned turkey's name was Reggie, so there's no way the adult Jake would know Reggie's name when they first meet.
Plot hole: The premise of the movie is that a group of this man's genetic offspring have united to learn his identity. He receives a stack of the bios of those in the lawsuit. One of the children he visits is severely disabled in a nursing facility and would not have been capable of joining the lawsuit.
Plot hole: Gerry's wife uses a rocket boot to break through a window and then slides down a curved wall to get to their son. She does so gracefully and takes off running. Gerry slides and takes a hard tumble and rolls down, landing on the ground. The next shot shows Gerry running behind his wife and not too far away as they reach their son. Even if it was to show a little time passing, there was not enough distance between where they broke the window and their son for Gerry to have picked himself up and catch up to his wife before reaching their son, especially with his wife being a worried mom doing a full on sprint to her kid.
Plot hole: When Grug is trying to escape from the explosion behind him he sees Douglas and says "Douglas! Hey I know that guy!" This is not possible since he neither knew the name of the creature or was nowhere around when Douglas was with Thunk.
Suggested correction: Thunk might have told him who Douglas is.
Plot hole: Marshall isn't present in the flashback where Chow steals the gold from the black van. How did Marshall know that it was Chow who stole the gold?
Plot hole: When they leave the B+B Gary's car The Beast is left parked outside as they walk into town. Later in the film they get to The King's Head and The Beast is parked out of the back of the pub. It's later used to escape from the next pub when it is driven through the wall. The Beast should be still at the B+B.
Plot hole: During the final scare event, Mike gets a perfect score because Sully broke the simulator to allow the 6th scarer to get a perfect score no matter what. After the contest, the simulation resets and Mike pretends to scare the child in the simulator and it registers a perfect score on the scoreboard for the 6th scarer when it should really have registered a score for the 1st scarer, because the simulator had been reset.
Plot hole: After the tyre, with Higgins in it, bounces on top of the cop car you can't see anyone in the back. When the tyre is stopped and they open the back of the cop car, Braden is inside. They didn't have time to pick up Braden before stopping the tyre. (00:47:00 - 00:48:10)
Plot hole: When Gretel is going through the weed maze the first time to find one of Carlos' goons in the cage, Agnes' dog is gone. But just earlier, she told her dog to stay there right by the cage, and the dog did so, and did not leave the garden. Yet Gretel is there and the dog is not seen, nor does it show up or attack her, despite all the loud noise, leaving a trail of Skittles, and the whistling. It does not make any sense that the dog would have vanished and not attacked Gretel. The writing even missed out on a good action scene there.
Plot hole: If Chester's plan was to steal the machine the entire time why didn't he just have his people steal the machine while it was still floating in the air during the first film? There was plenty of time to capture it before the food started mutating so what was he waiting for if he needed it so bad?
Suggested correction: Because he wasn't there in the first film? He first made an appearance in this film, doesn't know how to work the machine without Flint, and how the hell would he even get it in the sky? He also didn't even know about it, or what happened to Chew and Swallow, again, until he made an appearance in this film. Not a mistake.