I keep mixing up which novels, but in the early TNG-relaunch books, either Death in Winter
or Before Dishonor
, there is a contradiction where Worf meets Janeway, then later claims he never has done.
The Q's backstory in the Q-Continuum
trilogy is incompatible with The Eternal Tide
. Kirsten Beyer admitted in a podcast that she ignored all prior Q novels when writing hers.
Cold Equations #2: Silent Weapons
references Ship of the Line
, an older novel contradicted quite a bit by DTI: Watching the Clock
(although I should point out, SotL has some continuity issues with TNG too)
Indistinguishable From Magic
is swept under the rug by Plagues of Night
and completely ignored by Cold Equations
. This was by editorial decree.
I should also point out that considering the immense depth and complexity of the Trek novelverse, contradictions inevitable and understandable. The writers do an amazing job keeping things largely consistent!