When Mark arrives for his first day at school in the sports car, he pulls into a space, parking almost on the parking space line. When he walks away from the car, it is shown properly parked and centered in the parking space.
During the party scene were Mike is trying to convince Alex to talk with the girl who Alex likes, Alex's collar flips up and down on the right side as the camera angles switch. Alex's collar would have been flipped up from Mike padding him on the upper back while they walk towards the girl.
When Mike/Mark is shooting free-throws before the second big game there are seven balls on the rack including one on the top tier, after he talks to the coach there are only five with none on the rack and there hasn't been time or the sound of another shot.
When Mark/Mike is comforting Maggie after Stan just broke up with her, the camera angle constantly switches in order for their faces to each be seen. When the camera is focused on Mike, Maggie's shirt is off of her shoulder, revealing her bra strap. When the camera is aimed toward Maggie's face her shirt is covering both of her shoulders.
When Ned comments on Mark's "douche-y" clothing in the hallway right after Mark is admitted to the high school, two students walk past (from right to left behind Mark) and sneer at his outfit. A moment later, the same two students walk by in the same direction, and this time the boy calls Mark a "douche".
Before young Mike makes his sandwich, he takes a stick of some sort of food and easy cheese out of the fridge. The camera is behind Mike when he starts spraying the cheese but you can clearly see that the yellow wrapper is still on the food. The shot changes to face Mike as he finishes spraying the cheese but the food wrapper is gone. Later when the shot returns to Mike, the food is back in the wrapper.
In 1989, Scarlett is pregnant with Maggie, yet in the present-day scenes Maggie is only 17. Although the movie was released in 2009, if you pay attention in the scene where the students are sending the video of the fight to each other, one of the cell phones clearly shows a date of 2007 for the movie setting.
When back in 1989, Ned runs in late for the team picture wearing wizard robes and referencing a hippogriff, it may appear to be nod to Harry Potter (which was not published until 1997, and 1998 in America). However, the myth of hippogriffs is not a Harry Potter original, having been around for hundreds of years. Ned also makes reference to being "Dungeon Master", making it obvious he was playing Dungeons and Dragons, which has been around since the 1970s (hippogriffs included).
In the scene on the morning after the big party, Ned and Mark (Mike) have a conversation and Mark (Mike) is wearing a red plaid shirt. In the very next scene, Mark (Mike) is wearing a blue shirt with a white undershirt. However, Mike tells Ned he needs his pants. If Ned had time to put his clothes on, Mike had time to change the shirt.
At the big game in 1989, Mike throws a basketball over his shoulder (as he walks off the court to go after Scarlett). The camera pans down to show it bouncing vertically on the spot, but a real ball would be bouncing further and further away.
The goof item below may give away important plot points.
Incorrectly regarded as goofs
In the movie at the part in the divorce court, Mark/Mike looks down at his paper several times and his eyes move across the page (indicating that he's reading) but when Scarlet goes to get the "letter" only an address is on it. This was simply done to give the impression that he was actually reading the letter, otherwise the judge would have noticed that he wasn't reading the letter and have him kicked out.