Janeway orders an away team to return to the moon to investigate the sight of Neelix's attack, she instructs Tuvok to send a security team with them, armed with type-3 phasers. A type-3 phaser is a phaser rifle, but the away team are all armed with standard type-2 hand phasers, even the security team.
Captain Janeway says "I have a great sympathy for what your race has endured." Later on in Fury (2000) after Kes had traveled back in time Captain Janeway says to Commander Chakotay "Do I detect a note of sympathy?" She is contradicting her previous statement to the Vidiians here in season 1's "Phage".
The replicators are supposed to be offline and not accessible, although Tom is able to replicate a medical instrument for the doctor. Although this most probably is just the 'food' replicators that are offline. This is the system of organic foodstuffs replicators, that includes food and the captains' coffee. The crew is on emergency rations because of this. The inorganic replicators such as those that would replicate a medical instrument are obviously unaffected.
As a proof of concept for the idea of holographic lungs for Neelix, the doctor makes himself permeable to Tom Paris' slap but is able to push buttons a moment later to make himself impermeable again.
Dereth clearly mouths the word "Vaphoran" in Voyager's transporter room and "Vidiian" was subsequently looped over it. Broadcast closed captions of this episode also use "Vaphoran".
At the beginning, Neelix and Chakotay are exploring the cave for dilithium. Shortly after Neelix says, "I think I found something", he continues to walk deeper into the cavern. Right after he says, "but it's right here" and begins to move to the right, the scene changes. As he is walking you see the shadow of a boom mic across his face, just before he says, "I'm in the cavern now, Commander".
When explaining to the Captain what happened to Neelix, Commander Chakotay says he was unconscious when they found him. However, Neelix was conscious and flailing in panic not only when he was found, but up until they were transported back to the ship and the doctor put him in an induced coma.