Near the beginning of the episode as Mulder and Scully are walking into the refugee camp, one of the refugee actors breaks character by trying to suppress a smirk right as he's about to go out of the camera's view.
Continuity: While reading from his report at the beginning of the episode, Mulder refers to Jack McAlpin as John McAlpin.
Jack is a common nickname for those named John.
In "Fresh Bones", just after the opening credits, the shot of the road that Mulder and Scully are driving down is stamped as "Highway 10, Folkstone, North Carolina". In "Aubrey", three episodes earlier, the same shot is used the first time Mulder and Scully go to visit Cokely, and the stamp says "Highway 377, Missouri/Nebraska border".
While Mulder, Scully, and the groundskeeper are walking through Folkstone Municipal Cemetery, there is a partially hidden but still conspicuous sign that reads "Vancouver Cemetery."
When Mulder chases Chester on the pier, the camera's shadow can be seen as it circles around him.
Mulder: Private John McAlpin, he was one of the few, the proud... the dead. Last week he wrapped his car around a tree, died on impact.
(Whilst prodding a Voodoo charm)
Scully: Mulder, voodoo only works by instilling fear among its believers. You saw the way Bauvais tried to intimidate me. The power of suggestion is considerable, I'll admit.. But this is no more magic than a pair of fuzzy dice.
Scully: We're not sure what happened. But there is a medical explanation for his condiition.
Mulder: I was surprised to get your card. I had assumed our last contact... would be our last. Why are you here?
X: Your investigation is faltering, Agent Mulder.
Mulder: I've got a renegade Marine who may be violating every human rights provision...
X: These people have no rights. In 24 hours all access to Folkstone will be restricted to military personnel. No press, no third-party monitoring.
Mulder: What about Scully and me?
X: You'll be called back to Washington on a priority matter.
Mulder: They're making the camp invisible. Why?
X: In case you haven't noticed, Agent Mulder, the Statue of Liberty is on vacation. The new mandate says if you're not a citizen you'd better keep out.
Mulder: What do you know about zombies?
Scully: Well I hope you don't intend to tell Robin McAlpin that she married one.
When Colonel Wharton performs his voodoo ritual at the end he says in French: "To the spirits of the stars. The spirit of the moon."
"Fresh Bones" was the highest-rated episode of the first two seasons.
The groundskeeper's dog, Wong, is named after the writer James Wong, who had just left the show.
Film Reference: The Serpent and the Rainbow
The final scene with Wharton trapped inside the coffin mirrors the final scene from the Wes Craven movie which was based on a Wade Davis book about his experiences in Haiti.