When Darkling has Kes hostage and walks her to the transporter pad, there is a shot where the pad is visible. Visible on this pad are pieces of the tape used when blocking out the scene.
When the Doctor and Kes beam off the ship, Kes steps onto the transporter pad, where red gaffing place marks are still visible.
Darkling shoots the crewman manning the transporter room with a phaser. In most cases, phaser fire anywhere on the ship is detected on the bridge. In this case the writers overlooked that detail.
When Darkling and Kes beam off the ship, Janeway realizes something is wrong with the doctor and says to check on B'Elanna, who is in sickbay. She never says to have someone check on the transporter engineer.
The doctor leaves Torres paralyzed in sickbay. When Kes later enters sickbay, Torres is not there.
When the Doctor shows Kes the various characters with whom he interacts in the holodeck, "T'Pau" almost knocks over the kal-toh (Vulcan chess) structure by bumping it with the piece she is supposed to be placing delicately.