You arent the only one that had this problem, and SoA2 isnt the only mod that has the issue. It is a known AI lag issue. With the SoA2 ships all of them have more than one weapon type. In fact most ships have 3 different weapon types. This contributes to the problem, because vanilla sins frigates usually only have one forward firing weapon, and we MUST use the same roletype, and statcounttype for the vanilla sins ship a mod ship replaces, or the AI doesnt function at all (wont build, wont expand).
All of the SoA2 ships use dynamic (fighter) movement. This may also be a contributing factor, because vanilla sins ships do not move like that. They just move to a position and stop to face their targets. With dynamic movement it is possible the AI wants to fire an aft firing weapon but the target is facing forward, so the AI has a seizure when that happens.
What i believe is happening is that the AI is trying to figure out which weapon, on which facing, on which target to use, and the AI gets confused, and stalls. Same thing happens on player controlled ships sometimes (ships jump into the well and just freeze for a while before attacking).
Sins AI is hard coded so we cant alter or tweak it. I dont think anyone knows yet how to fix this. Least not that i am aware of. We have been trying to get developer help on it. Plus we have been in vain trying to figure it out ourselves.
BTW which version of SoA2 are you using for which version of sins? If it is for Original Sins (not entrenchment, not diplomacy) then there is no dynamic movement, because original sins does not support it.