When Veronica (Kristen Bell) and Cassidy (Kyle Gallner) are up on the roof and the situation with Curly (Adam Bitterman) was revealed, Beaver is seen writing "VERONICA MARS" on Curly's hand, but doesn't completely close the loop in the 'R' in Veronica. In the beginning of the season however, the R loop is closed on Curly's hand.
When Aaron Echolls is being interviewed outside the courthouse, the first shot of him shows his top suit button unbuttoned. When the camera cuts back and for the rest of the scene, it is buttoned.
In Veronica's dream before the opening credits, Veronica's mom puts three pancakes on her plate. A few cuts later, after her father and she has a short conversation, her plate holds only one pancake.
When Veronica looks to see if her dad has called as she waits for him at the airport her phone shows that it is 9:12am while in the shot preceding and afterwards shows that it is clearly night time.
Duncan (Teddy Dunn) is said to be in Mollymook, Australia, however everyone around him has American accents.
When Woody Goodman goes to the bathroom, the sound of a fly unzipping is quite distinctly heard, but the character is wearing boxer shorts.