In the scene where Zeke and Charlie are running back to the vortex, Charlie's goggles move from being on his left side to behind neck to his right side. The goggles keep moving back and forth.
In the scene where we first see the geek's clothes stolen from his locker from the bullies, when he goes upstairs to ask for them back, we see a wanted poster for the snowsuit guys behind the bullies, but nobody knows about them yet, because the Minutemen have only used the time machine once, and they didn't have the snow suits yet. When they go back in time to save the geek, and he goes upstairs again and the bullies are waiting for him, the wanted poster is gone.
The profile of the burning tyre rolling out of the vortex doesn't match that of the tyres on the cart before entering the vortex.
The first day of school is said to be on September 3, 2005. However, Sept. 3, 2005 was actually a Saturday.
When the Minutemen are heading toward the vortex in the cart, you can see the tracks from the previous takes imprinted in the grass.