If the bug were only happening to fighter carriers (which are the ships that appear in the list twice with the same name), I might view the shiplist as a possible suspect when combined with certain missions. But that doesn't seem to be the case. It's hard for me to judge though as I've still never seen the bug.
A few mission-packs ago, some Evil Dave base assault missions had a problem where the AI would fight you for control of your ship. I noticed then that you would have two sets of weapons in you ship; one that you could fire and one that the AI could fire. I'd suspect this problem is similar that one. The difference being that now the AI controls both sets of weapons, and so reaches the decision to fire both sets at once. In the Dave missions I rarely agreed with the AI decisions for my vessel and thus I usually fired my weapons seperately from his. (when I could get my ship pointed in the same direction)
For information sake:
The Gorn get their fighters from Federation entries. Being second in the shiplist, they had but one choice for a donor.
-Herr Burt