This became much more observable while using the Gatling Emitter but I have observed it during server lags or debuffs that increase ability cooldown. I have also noticed this during "busy" combat situations where lag itself isn't noticeable. I click on my abilities rather that use key-binds, and during combat, I'll occasionally have an ability or two that fails to queue up, or takes longer to register the interaction and activate/queue.
I managed to capture an example with Trajectory Bending, one of the abilities frequently affected by this bug:
Trajectory Bending, one of the worst offenders.
EDIT: Duplicated due due to mix-up, better explanation over at
https://www.arcgames.com/en/forums/startrekonline#/discussion/1264459/skills-fail-to-apply-queue-under-certain-situations