When asked if he's worked on anyone famous, Christian says they 'almost worked on Joan Rivers once', This refers to the Season 2 finale- entitled Joan Rivers- where she came to McNamara/Troy to have her extensive plastic surgery undone (but ultimately decided against it).
The storyline that is suggested for Hearts & Scalpels- about the woman who has her labia transplanted onto her face- is based on a surgery done in the Season 2 episode Bobbi Broderick.
When Sean and Troy are packing boxes, the two items Troy hands to Sean are packed, but reappear on the table after the next cut.
This episode has a lot of references to previous episodes and events within the show's history:
Reference is made to the Season 1 episode Antonia Ramos when Sean mentions that the titular character was a drug-mule of Escobar's whose breasts got infected by the drug-filled implants.
There are several references to the Pilot episode, with Christian mentioning getting 'a Botox shot in the dick' from Escobar (and the eventual disposal of both Silvio Perez and, later, Escobar himself).
Sean mentions Escobar shooting Liz, which happened in the Season 1 finale Escobar Gallardo and also mentions the murder of Alejandro Perez in his living room (which happened in Merrill Bobolit).
Michelle and Christian talk about the stealing of Liz's kidney (in Shari Noble).
In the final scene, the intern mentions 'the Rosenberg case' (Sean and Christian separated a pair of conjoined twins in the Season 2 episode Rose And Raven Rosenberg) and Sean's 'son's ectrodactyly operation' (in Conor McNamara)
When James has the gun pointed at Michelle, she mentions that killing 'a drunk is one thing'. In the previous episode Reefer, James orchestrated the murder and organ harvest of a homeless man (also called Reefer).
Sean asks Merrily if she knew Marlowe. Debbie Lee Carrington (Merrily) & Peter Dinklage (Marlowe) appeared together in "Tiptoes".
At the beginning of the episode, Christian mentions Sean has 'a gift from Diana Lubey', the patient played by Catherine Deneuve in the previous episode- also entitled Diana Lubey- who asked for ashes to be placed into her breast implants.
When Christian is being haunted by his previous relationships, he sees Natasha Charles. Played by Rebecca Gayheart, she appeared in two episodes of Season 2: Natasha Charles and Trudy Nye. She was a blind woman who came to McNamara/Troy for prosthetic eyes. They began a relationship, but Christian's fear of commitment and intimacy led to them breaking up.
When Christian is being haunted by his previous relationships, he sees Abby Mays. Played by Rebecca Metz, the character appeared in the Season 3 episode Abby Mays. She came in to McNamara/Troy for extensive surgery and Christian said he'd sleep with her if she put a paper bag over her head, which she did!
When Michelle and Sean are arguing at the beginning of the episode, Michelle mentions returning 'to a crime scene'. When Escobar escaped in Merrill Bobolit, he left several dead bodies behind him.
When Sean first meets Faith, he mentions her coming in to McNamara/Troy for a tattoo removal. This was also shown in Faith Wolper, PhD.
Faith refers to 'the dream' where Sean and Christian were lovers– this featured at the beginning of Faith Wolper, PhD.
When Christian and Sean confront Faith, Christian mentions that he 'nailed her in this office'. This was toward the end of the season opener Cindy Plumb.
Annie in 2026 reminds Julia about the time she cut up her dolls' hands to look like Conor. This happened in the episode Blu Mondae.
When Annie in 2026 is talking about her 'emotional baggage', she mentions having a party to celebrate her first period. Her 'Princess Menses' celebration was shown in the Season 2 episode Mrs. Grubman.
Goof: Bobolit mentions his previous abuse of/addiction to inhaled anesthetics, specifying nitrous oxide. Nitrous oxide is actually a dissociative analgesic, which is not potent enough to provide general anesthesia for surgery patients. The effects wear off almost immediately upon cessation of inhalation. Bobolit was certainly under something stronger when he attempted to swap faces with Christian in Season 2.
Additionally, addiction to nitrous isn't technically possible.
When Sean and Christian go to see Escobar in the prison hospital, Escobar mentions that his face was "burned off" by a MS 13 gang member, this stands for Mara Salvatrucha, "Salvadoran Gang".
When Escobar mentioned Silvio Perez and dumping his body in a swamp, there is a flashback to the Pilot episode, where these events occurred.
When Sean and Christian go to see Escobar in the prison hospital, Escobar mentions them turning him into 'the FBI's most wanted'. This happened in the Season 1 finale entitled Escobar Gallardo.
Christian admits to sleeping with Kimber recently. This happens in the episode entitled Burt Landau.