Goof: When The Doctor is uploaded into the alien communications-grid, he dematerializes with his mobile emitter. But, since the mobile emitter itself is not holographic, it should remain and fall down. But after disappearing when The Doctor did, it did not reappear on the Prometheus, either.
Trivia: This episode has Voyager's first and only mention of the Dominion War, although the Dominion would be referenced in the next episode.
Goof: In the Prometheus' sickbay, The Doctor reveals that the ship is travelling at Warp 9.9. However, when he goes to the bridge to access environmental controls, the viewscreen shows a stationary starfield, which indicates that the ship isn't moving.
Trivia: Two unnamed Defiant-class ships are seen in this episode, adding to the known roster.
The Doctor: You hit the wrong ship!
EMH-2: It wasn't my fault.
The Doctor: Then whose fault was it, the torpedoes? You're supposed to tell him what to do!
The Doctor: I'm as close to sentient being could hope to be. I socialize with the crew, fraternize with aliens, I've even had sexual relations.
EMH-2: Sex!? How's that possible? We're not equipped to...
The Doctor: Lets just say I made an addition to my programming.
EMH-2: Perhaps before you leave you could download those subroutines into my database.
The Doctor: We'll see.
Janeway: Good luck, Doctor
The Doctor: There's that word again.
EMH-2: What are you doing here?
The Doctor: If you disengage your vocal subroutines for one second, I'll explain.
The Doctor: You know, you really should keep a personal log. Why bore others needlessly?
EMH-2: My brilliant existence cut short. No time to explore the universe. No time to smell the roses. No time for...sex.
The Doctor: I was saving Voyager from annihilation when you were only a gleam in your programmer's eye.
Prometheus Computer: Specify attack formation.
The Doctor: Attack Pattern... alpha?
Prometheus Computer: Specify target.
(The Doctor & EMH-2 look at each other)
The Doctor & EMH-2: The Romulans!
EMH-2: What are they doing?
The Doctor: Firing on us!
EMH-2: They must think Romulans are on board.
The Doctor: They're right!
The Doctor: Stop breathing down my neck!
EMH-2: My breathing is merely a simulation.
The Doctor: So is my neck! Stop it anyway!
Paris: I'm a pilot Harry, not a doctor.
This is an allusion to Dr. McCoy's famous "I'm a doctor, not a..." lines from The Original Series.