For me, it all depends.
If the contradictions are within a group of works that are clearly supposed to be in continuity with each other, then yes that annoys the hell out of me and will greatly impact my ability to enjoy the story regardless of how good the rest of the story may be. For example: Things apart of a series like the DS9-R, Voy-R, TNG-R etc if those books start contradicting each other that's a problem. Like Steve Roby
, I found Before Dishonor
's contradictions of Q&A
Then let's not get into contradictions within the same book. If a shuttlecraft was destroyed on page 5 then was seen flying around on page 200 without some sort of time jump or other good explanation I'd have a problem with that.
As for things not specifically set in the same continuity (even if in the same universe) I don't have much issue with that sort of contradiction. All one needs to do is apply the "Myriad Universes" concept. So Federation
still *ahem* "happened" as did First Contact
, they just occurred in different Universes -- er um, Quantum Realities.