When Veronica (Kristen Bell) drops the boys off and remains in the car to talk with Troy (Aaron Ashmore), she has her top draped across her shoulders. During the close-up of Troy however, you can see that she is wearing only her t-shirt.
When Veronica (Kristen Bell) is yelling at Troy (Aaron Ashmore) about his past, he closes the locker at one point and the scene cuts to her right after and she says "Don't even!" but the locker is still open. When the scene cuts back to Troy the locker is again closed. You can even hear the locker slam on the part where we can see it open when it cuts to Veronica.
Near the end, when Hank Zigman approaches the border, we see the border guard take the sheet sent by Veronica Mars earlier. Under this page we see an information sheet on a certain "Raphael Bruno", which was intended to be written in Spanish. However, under the word "Atencion", we can clearly see: "All this stuff is suppose to be in Spanish, however the person who usually translates for us is on vacation, so just act like this is in Spanish."
Just after Rebecca James drops and shatters the ceramic bowl in the kitchen, Veronica bumps the counter. It wobbles, revealing it to be a prop, as opposed to a sturdy kitchen counter.
When Veronica is driving through an intersection, a green light is visible for the cross street indicating that she's running a red light.
Veronica (Kristen Bell) logs into the P.I. website using her own name, but she doesn't have a P.I. license yet.
When Troy is talking to Shauna on the phone, in his dad's car, you can see the boom mic bouncing in the upper right hand corner.