I've been leveling a KDF science alt, and when I got to Captain, I moved into a Pach raptor. Ever since I've used this ship, I haven't been able to use Hazard Emitters 2, Starship Dampening Field, or Subnucleonic Beam (The icons were all darkened, like they are in sector space). I didn't have any debuffs, and my aux was at 41. I wasn't targetting anything either. It affected me in and out of combat. I've tried retraining HE, using another BOff with HE, and putting more points into it.
I'm hoping that when I get to tier 5, and get another ship, it'll go away, but it may not.
EDIT: Other science skills like Tractor Beam and Sensor Scan still work for me.
EDIT: Wow... I forgot to equip a Deflector Dish.... I feel stupid now.
And I thought I was being thorough in checking for a way to fix the problem....