When Brendan is in Tug's trunk on the way to see the Pin for the first time he opens up the trunk to see where the Pin lives. He clearly does not have his glasses on while looking out from the trunk. Yet, in the next scene the camera's vision of the Pin is very blurry until Brendan puts his glasses back on. This makes it impossible for him to have been able to see the numbers on the mailbox without his glasses on.
After Brendan's confrontation with Dode in the football field, he falls on the grass and briefly passes out. When he wakes up and hears Laura's horn, his clothing is dirty. When he reaches the tunnel to meet with Tug, The Pin, and Dode, his clothing is clean.
After his first encounter behind the Coffee and Pie, Brendon is seen hiding behind a bush as he follows someone. As he gets up to walk away, you can clearly see a large red abrasion on the left side of his face that isn't in the previous or following shots.
The second time that Brendan and The Brain meet at The Brain's spot. As Brendan asks The Brain about the words that Emily spoke on the phone, two students walk behind them. A few moments later, the exact same pair of students walk behind Brendan, going in the same direction.
When Pin enters his house while Tug and Brendan are talking at the kitchen table, we can see that he is wearing what appears to be white sneakers. Later on in that scene, there is a shot from under the table and we can see he is wearing the big black orthopedic shoe he usually wears.
As Brendan is calling the phone number on the "Halloween in January" party invitation he pulled from Kara's dressing room mirror, his Timex wrist watch reads 10:45, while in the background the digital alarm clock on his nightstand reads 11:53.
When Brendan meets Dode on the football field, he falls down and his jacket gets quite muddy along the right arm and right side. The next scene is Brendan going to the tunnel at 4:00 p.m. for the meeting, and the jacket is perfectly clean.
When Brendan is led into the Pin's office by Tugger: there are several boys lined up on either side of the corridor right up to the door of the office. In the next shot from within the office the door is left open, but no one can be seen in the corridor.