Factual error: At the onset of the episode, Christian and his blind girlfriend decide to go to a movie rental place. While Christian goes inside, he leaves his gf in the car and the song "Love Will Keep Us Together" by Captain and Tenille is playing. During this time, two young guys pull up in a van and find out the girl is blind and then decide to strip Christian's car of all 4 wheels and the front end. Christian comes out about three minutes later (the end of the same song is nearing) to see his car sitting on 4 jacks and void of any wheels or front end. Given the time that Christian is gone which is just a few minutes, it is nearly impossible for even a team of multiple seasoned pro thieves with the most sophisticated auto equipment to disassemble part of a car (and those specific parts) in that small amount of time, let alone two kids just passing by deciding to do so on the spur of the moment.
Audio problem: During the scene right after Julia was looking at Jude's photos and then is on the couch talking to him, pay close attention to the shots behind Jude. At least three different times, when Jude is talking to Julia about interning at her husband's office, we see Jude's lips moving but hear no words, or, he is speaking but his lips aren't moving at all.
Continuity mistake: During the scene where Sean first meets Sophia Lopez in his office and he is about to counsel her, one camera view has Sean looking down at his notes and writing something, then looking up at Sophia as he begins speaking. A split second later, now from the opposite camera view, Sean looks up again and hasn't begun speaking yet.
Plot hole: By the end of Season 3, it is revealed that Dr. Costa was the Carver. It is important to also note that the first introduction to the Carver came around mid-Season 2, and there were more than a handful of victims - including Dr. McNamara himself - all in the Miami area. One huge discrepancy during that initial time period though is that Dr. Costa was living in Atlanta, running his own plastic surgery firm (we know this because Julian flew him in from Atlanta to work on Dr. McNamara). While not impossible, it just doesn't seem logistical for Dr. Costa to commute back and forth from Atlanta to Miami to commit these crimes, all while still working/running his practice in Atlanta, especially in such short spurts of time.
Other mistake: In episode 5-21: "Allegra Calderello," Allegra discusses with Shawn and Christian the fact that the show-within-a-show, "Hearts and Scalpels," featured a character based on her, called "pussy lips" because Allegra had her lips reconstructed with her labia. However, in episode 5-1: "Carly Summers," Shawn and Christian referred to their one-time patient as "pussy lips," but the network censors refused to air the word "pussy," and the euphemistic phrase "lady cha-cha" was used on the air instead. So Allegra would never have seen a character called "pussy lips."
Audio problem: When Christian is returning to the office and sees a crowd of people outside hoping to see Agatha (who they believe has the stigmata of Jesus Christ), he runs into a couple with their infant. Christian asks if their baby is sick, and the couple shows him the backside of the infant where it has a vertebrae "tail", and they then ask him if they can see Agatha. During this sequence, we can hear loud crying, but various camera shots show the baby's face and she/she is not crying.