I just noticed this today, so I don't know if this just recently changed, but I discovered two science skills that are not being affected/buffed by equipping the proper science console:
Tyken's Rift is not being affected by Collimator (+ deflector dish)
Photonic Shockwave is not being affected by Holomatric Diode (+ photonic theory)
Tyken's power description does not list the systems that it's affected by in its description, but at the beginning it does mention that it uses System: Deflector Dish. Obviously it uses Spatial Anomaly (and those consoles do work with it). It would be nice if this power had a list of the systems/skills that actually affect it like most other powers have listed at the bottom of their description.
The same cannot be said for Photonic Shockwave: the power description clearly says it's affected by Emitters, Deflector Dish, and Operations Training. But in our character's skill window, Photonic Shockwave is listed as one of the powers improved by training in Photonic Theory, and is also where we get Photonic Shockwave 3 if we fully spec in it. Shockwave IS being affected by +Deflector Dish, but NOT +photonic theory consoles.
I've tried having 0 science consoles equipped, checking values, and then equipping only 1 of the corresponding consoles and rechecking values and in each case there's no change. I tried zoning and checking again and there is still no change.
If I'm in error somewhere, please let me know, but when it states in a description that a specific ability is improved by a specific system or skill, I take it as fact.
I submitted a ticket when I discovered Tyken's Rift not being affected by deflector dish (but I don't know the ticket number) and decided to write here when I discovered Photonic Shockwave was suffering a similar problem.