When Bones goes into her office with Booth, she puts her jacket over the back of the chair to sit down, but the jacket falls off the back of the chair and into the seat. In the next shot when she has sat down, the jacket is on the back of the chair.
When Bones and Booth are in the diner before Fran Duncan comes in to confess to her husband's murder, Bones takes a sip of her drink which is about a quarter full of liquid, but when she puts the drink down, the glass is full.
(at around 28 mins) Hodgins enters and describes, to Booth and Saroyan, a rose that he is holding as an "English Alba Rose," a "climbing variety." While it is true that the English Alba Rose is a climbing variety, the rose that Hodgins is holding is a long stem variety.
When Booth asks how much of the garbage they're going to need, you can see the camera is behind some type of Plexiglass. There appears to be a scratch right where his glasses are. When he throws the garbage towards the camera it clearly hits the Plexiglass before the scene ends.
During the opening scene, just after Hodgins says the victim has been dead for 3 weeks, a fly is seen crawling around on the lens of the camera.
At around 23 minutes in, Bones and Cam are discussing what they would like Hodgins to do next. When Cam says that she would rather he continue looking for the pipe, she explains that "It might have Kevin Dylan's DNA on it." The character she is referring to is Kevin Duncan. She mixes up his last name and the victim's first name, Dylan.