Some of my favourites:

1. If you build a shipyard above Mars it's automatically called Utopia Planitia.
2. Riker and Sisko's beards come and go in line with the canon year.
3. Most of the time the first ship you build of a class has the same name as that class.
4. Borg ships do their best to attack Earth via Wolf 359

What others have people noticed?