Hmm, I'm getting a crash that I'm pretty sure is Mayasuran related. I think this because it always happens when I am inside the Mayasura system, and in several cases I've observed it to occur when the Mayasuran navy engages an enemy. My guess is that it is trying to load one of the ships, but failing in some way.
Spoiler
7563678 [Thread-3] ERROR com.fs.starfarer.combat.CombatMain - java.lang.ArrayIndexOutOfBoundsException: -1
java.lang.ArrayIndexOutOfBoundsException: -1
at java.util.ArrayList.elementData(Unknown Source)
at java.util.ArrayList.get(Unknown Source)
at com.fs.starfarer.api.plugins.impl.CoreAutofitPlugin.doFit(CoreAutofitPlugin.java:464)
at com.fs.starfarer.api.impl.campaign.fleets.DefaultFleetInflater.inflate(DefaultFleetInflater.java:422)
at com.fs.starfarer.campaign.fleet.CampaignFleet.inflateIfNeeded(Unknown Source)
at com.fs.starfarer.ui.impl.StandardTooltipV2.createFleetTooltip(Unknown Source)
at com.fs.starfarer.campaign.E.o00000(Unknown Source)
at com.fs.starfarer.campaign.CampaignEngine.advance(Unknown Source)
at com.fs.starfarer.campaign.CampaignState.advance(Unknown Source)
at com.fs.starfarer.BaseGameState.traverse(Unknown Source)
at com.fs.state.AppDriver.begin(Unknown Source)
at com.fs.starfarer.combat.CombatMain.main(Unknown Source)
at com.fs.starfarer.StarfarerLauncher.o00000(Unknown Source)
at com.fs.starfarer.StarfarerLauncher$1.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
If I manage to leave the system rapidly enough after loading the game, the error doesn't occur, but if I repeat my prior actions, or simply stay in the system, it's a very consistent error.
This is the only faction mod I am using, and it is up to date. I really enjoy the balance and design of the mod, so I am hoping not to have to remove it when I start a new game.