Parturition - S2-E7
Revealing mistake: On the bridge, as Tuvok monitors and reports on the pursuing ship's weapons, you can see what looks like a wristwatch on his right wrist as he works the controls. (00:35:35)
Dreadnought - S2-E17
Continuity mistake: Dreadnought states there are fifteen priority targets approaching. On radar sixteen Rakosan ships are displayed. Then just before the Dreadnought attacks (and destroys three of) the approaching ships, there are a total of nineteen Rakosan ships displayed on radar.
Repression - S7-E4
Other mistake: In the 3D cinema scenes in the Holodeck, Tom Paris and B'Elanna Torres can be seen using blue/cyan anaglyph glasses and the movie screen can be seen to be in blue/cyan also. This is fine and to be expected. However the shot in which the projection room can be seen behind the couple show the projection is through magenta/green filters. (00:03:30)
Other mistake: They show Kes as a baby but her ears are human. (00:42:25)
Basics (2) - S3-E1
Deliberate mistake: After Voyager's secondary phaser banks overload, everyone on the ship seems to be severely injured, but Seska's baby is perfectly fine. This is likely to be a conscious decision by the writers. (00:40:30)
Mortal Coil - S4-E12
Continuity mistake: The shuttle is "parked" in the nebula to get a protomatter sample, and the nebula is visible in all windows. After the shuttle is hit, the camera looks at Tom, and the view in the window is the black of space with stars, rather than the bright nebula.
Factual error: The event horizon of a quantum singularity (aka black hole) is not a physical barrier you can punch a hole through but a theoretical one, which can't be escaped from without faster then light travel.
Character mistake: When trying to trap the energy mass they created, B'Elanna announces, "Now it's trapped on three sides," to which Paris replies, "It's changing course. Heading for the open side." Since we function in 3-dimensional space, unless they are trying to trap it in a triangular-based pyramid, the number of "sides" to be concerned with is six.
Continuity mistake: In season 6 episode 10 'Pathfinder', Admiral Owen Paris has the rank of Full Admiral. In season 7 episode 6 'Inside Man', the same Character is seen as being only a Vice Admiral. In the season 7 season episode 'Endgame', the last episode of the show, he is once again seen as being a Full Admiral.
Revealing mistake: If you look closely at the hot air balloon, in the shot before the message is attached to it, you can just see a wire holding it up.
Answer: It's been established that the reboot doesn't affect anything in the original timelines of any prior series. The alternate timeline of the new films does not change anything that came before.
Captain Defenestrator