There is a serious bug with the Missiles. Load the save. On the next turn the Lizards will arrive, you can either attack them or they will attack you. In combat do the following. Select a Terran ship, fire missiles, move one spot, and you can fire missiles again in the same combat round, move gain, and you get to fire again. This would allow me to unload my entire payload on one turn, it would be devastating to the AI Edit. The Condor behaves normally, it is my own designs that have this property of being able to fire multiple times, needless to say, I like it... but it must be removed.
Still present in the stable release... I don't see the AI ships or found ships having this "repeat" missile fire...
Here is a new save file, perhaps it will help you isolate the problem. Process the turn and a Moltar FF will arrive at Isrips Use your own Terran Frigate to fire a missile first, then move slightly and fire again, I was able to get off three shots in a single turn with that Frigate.