Brennan stated in a previous episode that she was in foster care until her grandfather got her out. Now it is stated that to keep their family safe, her parents changed their names. Brennan couldn't have a grandfather who got her out of foster care if they had changed their names for protection.
Zach states that Brennan joined the Jeffersonian in 1998, putting her there approximately 8 years. However, in episode 8, Dr. Goodman mentioned that he only hired her two years ago.
In the fourth chapter, there is a discrepancy regarding the movie ticket shown from 9/22/93 for the movie 'The Fugitive'. All dates except for the biggest one of the ticket read 4/22/93 instead of 9/22/93, even the date for the time that the ticket was printed.
The movie ticket for "The Fugitive" found on the body of Dr. Brennan's mother has a very visible "R" rating stamped on it. "The Fugitive" was rated PG-13.
When examining the movie ticket discovered in Bones' mother's grave, Angela says it's dated 'September 2, 1993', but the ticket shows a date of April 22 (04/22/93). The day of the week on the ticket (Wednesday) is also incorrect: April 22, 1993 was a Thursday, not a Wednesday.
At the very end of the episode, when Bones gets three beer bottles out of the fridge, they all have tops. She then simply walks across her kitchen and hands one to Booth and one to her brother, never stopping to open the beer. Even if they were twist top bottles, there is no way she could have gotten the tops off that quickly or silently.
When Angela and Hodgins are showing Brennan the movie ticket, there are two different versions on the screen. The actual ticket is on the left of the screen and a digital copy on the right. The actual ticket has the same information Angela reads to Brennan. Rialto Theater, 9 pm showing, September 22nd, 1993. However the digital copy shows 4/22/93, not 9/22/93.
When Brennan plays the message from her father, while the answering machine is clearly hooked up, there is no read out on the LCD screen on the phone, indicating that the phone itself is not hooked up.
When Brennan asks Booth where he found her brother, Booth says "Morehead City, NC." Morehead City is a coastal town without a permanent amusement park. There are various amusements, but no park. Thus the sound design would need to include general coastal sound effects. Morehead City is also 6 hours from Washington D.C. Since Booth and Brennan travel to meet Russ in the late evening at the end of the episode, it would have been the middle of the night or the early morning by the time they reached Morehead City.
When Bones is looking at the DNA test results, she points to the first three results and says that they are hers, Russ', and her mom's, when they aren't. The first one is their mother's, the second one is an unknown person and the last two are her and her brother's.