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.
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. (00:21:45)
Revealing mistake: In the scene where Barclay 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).