I dont really know if this is a bug or not, but when u choose for example 2 different support ships with all spec weapons researched it does not show them all. Only a random selection of 4 :S
That should be fixed IMO, cause if you want to fire a specific special weapon you would have to select a certain support ship and then give it orders. And that is just annoying lol, would be much better if you could see all your spec weapons when u select a group of ships  
If you dont know what I mean, here is a screen about it:
(I have 2 different support ships in my fleet and I can only see 4 spec weapons)

i've noticed this for the feds but for them it doesn't happen all of the time, most probably depends on how many other specials need to be displayed.

this could be an A2 engine problem ( GUI limitation) or something, perhaps its unavoidable    *shrugs*

I'm currently completely redoing the special weapons stuff. some if these issues might be fixed with it. i will do my best