Revealing mistake: In the scene where Barcley reappears on the transporter with the crewmember, they both fall to the ground. The transporter chief had put up a forcefield around the transporter chamber, in case something goes wrong. However, when the crewmember falls to the ground, his foot goes right through where the forcefield is meant to be. It is still active, as only a few seconds later we see it being deactivated.
Continuity mistake: In the episode 'Yesterday's Enterprise' (season three, episode 15), watch the final scene with Geordi and Guinan in Ten-Forward. Although time and the universe has returned to normal, Geordi is still wearing the uniform from the alternate timeline (note the sleeve detail, and the extended neck piece).
Revealing mistake: In season 5, "The Game," the brainwashed crew members hold Wesley's eyes open to force him to see the mind-controlling game. Their intention is to prevent him from closing his eyes, which would protect him from the device. While they are doing this, he blinks.
Visible crew/equipment: Near the start, just as Riker says "You have all the time you need.", the engine consultant stops and turns around. As he does so, look above his head and you can see a microphone hanging down. The camera quickly adjusts so it's not visible any more. [Not visible in the remastered Blu-ray version].
Other mistake: When Q the Judge enters on his throne, at one point, the hydraulic arm the throne is on is visible, despite being black to blend in. Conversely, in "All Good Things...", the final episode, the arm is missing having been matted out by CGI techniques.
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Factual error: Shelby announces the Borg have entered Sector 001, and we get an exterior shot of the Borg ship flying past Saturn. The problem is that the Borg are approaching from the side of the planet illuminated by the sun, meaning they would actually be moving AWAY from Earth rather than toward it.