- the canon itself isn't perfectly consistent
- programmers/artists/writers/directors/producers are human, and humans make mistakes
- TV shows, movies, and games have limited budgets; there's not enough time/money to check everything
- new people working on a franchise product want to put their own creative mark on the franchise
The concern of some Star Trek fans is that Abrams & Co. are going that latter route, that they're changing things just to be different or out of laziness or out of hubris, that they're compromising the established history of Star Trek when they don't have to.
This does happen. Directors certainly do take liberties with franchises -- look what David Fincher did in the third movie of the "Alien" saga.
But is something like this happening with Star Trek XI? I don't know. Abrams and his minions could be respecting the lore or desecrating it; I have no idea which is the case. I'm not personally expressing any warnings that the new movie will suck in this respect because I don't feel I have enough information at this time to come to such a conclusion.
All I'm saying is that the concern some fans are feeling right now is not irrational. They may turn out to have been wrong, but at this moment in time, given the information available, their concerns are not unreasonable. Hollywood people have legendarily strong Reality Distortion Fields operating....
Is the same true of the designers and producers of major MMORPGs like Star Trek Online? I guess we'll just have to wait and see.