Basestar subsystems are really pissing me off.
Try reading my guide just posted on the forum. It might shed some light on how to really hit those Toasters
My guess is you're having trouble with the targeting system? Destroy a Heavy Missile Turret (HMT) and it auto-locks on to a Light Missile Turret (LMT) without you really knowing about it? Try pressing "N" to target the objectives instead of cycling through all the Turrets
Also, make sure you have a clear shot at the target. HMT's can only really be hit from the "inside". By this I mean you have to get up close and personal with the Basestar. The Basestar has armor on its "spikes/legs/tentacles/whatever-you-call-them" so you have to hit the exposed side (i.e. The one with all the stuff on it or the "inside".)
Hope that helps!