Penetration mods are useless on these guns:
Adas Anti-Synthetic Rifle (I just found this one out myself a few days ago!).
M-37 Falcon.
Striker Assault Rifle.
Acolyte.
Scorpion.
Geth Plasma Shotgun.
Graal Spike Thrower.
Venom Shotgun.
Kishock Harpoon Gun.
Krysae Sniper Rifle.
Sniper Rifle Spare Thermal Clip mod is useless on the Collector Sniper Rifle.
SMG Heat Sink mod is useless on the Collector SMG.
Shotgun Smart Choke is useless on the Venom Shotgun and the N7 Crusader, and of very little use on the Reegar Carbine (it only improves the pellet spread, not the range) and the Geth Plasma Shotgun (it only benefits uncharged shots).
Particle Rifle has zero recoil, so gains nothing from Assault Rifle Stability Damper.
Javelin already has an x-ray scope, so gains nothing from scope upgrades.
And I wouldn't expect a Pistol Cranial Trauma System to do much on an Acolyte or Scorpion either.
Does that help?
And for what it's worth, I agree that non-functional mods should have been non-equipable.
21/01/14: Edited to add PPR and javelin, rephrase the GPR, and remove the Graal.
Graal
does benefit from the smart choke, my bad.
Thanks for the corrections cato.
Edited by Evil Mastered, 21 January 2014 - 05:18 AM.