While this WAS on a modded game, I think this would apply to vanilla as well, hence why I am posting here.
Basically if you auto assign weapons when you have more than 25 weapons, the game crashes with this error:
Spoiler
144968 [Thread-3] ERROR com.fs.starfarer.combat.CombatMain - java.lang.NullPointerException
java.lang.NullPointerException
at com.fs.starfarer.coreui.refit.wgd2.Object.updateCheckboxes(Unknown Source)
at com.fs.starfarer.coreui.refit.wgd2.WeaponGroupDialogV2.actionPerformed(Unknown Source)
at com.fs.starfarer.ui.k.buttonPressed(Unknown Source)
at com.fs.starfarer.ui.I.Ò00000(Unknown Source)
at com.fs.starfarer.ui.I.processInput(Unknown Source)
at com.fs.starfarer.ui.k.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.Q.processInput(Unknown Source)
at com.fs.starfarer.ui.v.dispatchEventsToChildren(Unknown Source)
at com.fs.starfarer.ui.v.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.Q.processInput(Unknown Source)
at com.fs.starfarer.String.I.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.Q.processInput(Unknown Source)
at com.fs.starfarer.ui.v.dispatchEventsToChildren(Unknown Source)
at com.fs.starfarer.ui.v.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.Oo0O.processInputImpl(Unknown Source)
at com.fs.starfarer.coreui.refit.wgd2.WeaponGroupDialogV2.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.Q.processInput(Unknown Source)
at com.fs.starfarer.ui.v.dispatchEventsToChildren(Unknown Source)
at com.fs.starfarer.ui.v.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.Oo0O.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.newui.K.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.Q.processInput(Unknown Source)
at com.fs.starfarer.ui.v.dispatchEventsToChildren(Unknown Source)
at com.fs.starfarer.ui.v.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.Oo0O.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.newui.Stringsuper.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.Q.processInput(Unknown Source)
at com.fs.starfarer.ui.v.dispatchEventsToChildren(Unknown Source)
at com.fs.starfarer.ui.v.processInputImpl(Unknown Source)
at com.fs.starfarer.ui.Q.processInput(Unknown Source)
at com.fs.starfarer.campaign.CampaignState.processInput(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)