I'm a MT Sith Juggernaut for my guild and I can say that the GCD bugged is NOT caused by parry/dodge/deflect, but it does LOOK like it does.
I can pretty much say that this is a general bug because I've had it happen rarely on my non-tank characters because I'm OCD and hit the buttons repeatedly.
1. I've had the GCD bug happen several times on the Soa fight in eternity vault, in this fight this boss does NOTHING you can parry/dodge/deflect (Verified by the fact that retaliation NEVER triggers)
2. I've jumped into large packs in HM's and had zero issues firing off my abilities, and when you're rolling with around 30% defense jumping into packs of 3-5 it's almost impossible to NOT parry/dodge something.
I can tell you the main thing that helps me avoid the GCD bug is DO NOT SLAM YOUR BUTTONS. This is extremely difficult for me since I'm fairly OCD and want my abilities to fire as fast as possible.
Honestly it looks like the problem is more in the ability queuing system over parry/dodge. To give an example, my normal opener on trash packs in HM's was to Force Charge->Smash and I would be slamming my smash button frequently while force charge was still executing, and a LOT of times I would end up GCD bugged. Now I do my best to hit charge, then right before the GCD is done I hit my smash button ONCE and just try my damndest to leave the button alone. This seems to solve almost all of my problems.
There's also a sync issue with the client/server where you won't actually be where the server thinks you are, and you'll try to fire off abilities but can't. This can be seen pretty frequently on mobs that like to stun/choke you on their first action if you use force charge to open. You can solve this by using force charge again, or having a friendly sorc use their grip ability on you (Intervene doesn't seem to work as well for fixing this issue).