My theory is it depends on how much it interferes with credibility and story. Or the viewer's perception of credibility and story. But some fans are probably just fanatics and "purists".
I think certain minor things are not enough to ruin a show or episode, but then again some minor things can have a negative effect down the road.
For example, I know the Nu Trek movies are considered a separate timeline, but I always thought having Kirk going from cadet to captain of the Enterprise at the end of the movie, and the others from cadets to senior officers played with credibility a little too much.
Sulu was a nervous raw cadet who needed help getting the ship into warp, by the 2nd movie (a year later) he's acting captain of the whole ship. There are no older, senior officers on the ship at all and all the senior staff are filled by Uhura, Chekov McCoy and Sulu, most of them were previously raw cadets.
It was a strain on credibility. Maybe because of the original "cannon" where they all worked their way up into their positions, whereas here, they are suddenly all plugged into their positions instantly.
I had a sneaking suspicion part this ultimately had a negative affect on the series later on and the fans lost some interest. The series felt like it skipped over a lot of things and filled in everything else with action and explosions.
Everything was so rushed and put together so fast, all the dynamics, the Spock/McCoy thing, Uhura as a person, Scotty and his engines etc., was missing badly.