During a battle, any ship firing with a phase lance will crash the game. It's probably a problem with a mod but the facts that it's a vanilla weapon that causes the crash give me no clue about which one is implied.
Spoiler
520439 [Thread-7] INFO sound.oo0O - Cleaning up music with id [faction_generic_market_01_neutral_var01.ogg]
520750 [Thread-9] INFO sound.oo0O - Creating streaming player for music with id [BFG3.ogg]
520752 [Thread-9] INFO sound.OooO - Playing music with id [BFG3.ogg]
523756 [Thread-3] INFO org.histidine.chatter.combat.ChatterCombatPlugin - Adding ship Nephi-Prizon, isEnemy 0
523757 [Thread-3] INFO org.histidine.chatter.combat.ChatterCombatPlugin - Adding ship HSS Mephitis, isEnemy 0
523757 [Thread-3] INFO org.histidine.chatter.combat.ChatterCombatPlugin - Adding ship Sword of Retribution, isEnemy 0
544328 [Thread-3] INFO sound.oo0O - Cleaning up music with id [miscallenous_corvus_campaign_music.ogg]
544331 [Thread-7] INFO sound.oo0O - Cleaning up music with id [BFG3.ogg]
544607 [Thread-3] ERROR com.fs.starfarer.combat.CombatMain - java.lang.NullPointerException
java.lang.NullPointerException
at com.fs.starfarer.combat.entities.ship.A.G.this.super(Unknown Source)
at com.fs.starfarer.combat.entities.ship.A.G.createBeam(Unknown Source)
at com.fs.starfarer.combat.entities.ship.trackers.E.super(Unknown Source)
at com.fs.starfarer.combat.entities.ship.trackers.O0OO.super(Unknown Source)
at com.fs.starfarer.combat.entities.ship.trackers.O0OO.super(Unknown Source)
at com.fs.starfarer.combat.entities.ship.trackers.E.super(Unknown Source)
at com.fs.starfarer.combat.entities.ship.A.G.advance(Unknown Source)
at com.fs.starfarer.combat.systems.G.o00000(Unknown Source)
at com.fs.starfarer.combat.systems.G.advance(Unknown Source)
at com.fs.starfarer.combat.entities.Ship.advance(Unknown Source)
at com.fs.starfarer.combat.CombatEngine.advanceInner(Unknown Source)
at com.fs.starfarer.combat.CombatEngine.advance(Unknown Source)
at com.fs.starfarer.combat.CombatState.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)
544778 [Thread-9] INFO sound.oo0O - Creating streaming player for music with id [DawII1.ogg]
544781 [Thread-9] INFO sound.OooO - Playing music with id [DawII1.ogg]
Spoiler
"$$$_lightshow",
"pantera_ANewLevel20",
"anotherportraitpack",
"raccoonarms",
"bsgportraitspack",
"beyondthesector",
"BSC",
"CWSP",
"CSP",
"chatter",
"lw_console",
"diableavionics",
"dronelib",
"exshippack",
"fluffships",
"sun_fuel_siphoning",
"hte",
"ImperialNavy",
"IndEvo",
"interestingportraitspack",
"kadur_remnant",
"kingdomofterra",
"LTA",
"lw_lazylib",
"ArkLeg",
"MagicLib",
"missingships",
"more_hullmods",
"nexerelin",
"pn",
"wyv_planetaryShieldAccessControl",
"PulseIndustry",
"rotcesrats",
"sanguinary_autonomist_defectors",
"tahlan_scalartech",
"SEEKER",
"speedUp",
"superweapons",
"timid_supply_forging",
"tahlan",
"Terraforming and Station Construction",
"exalted",
"star_federation",
"transfer_all_items",
"US",
"URW",
"vic",
"vayrashippack",
"whichmod",
"audio_plus",
"astroidships",
"shaderLib"
I don't know if it is correlated but I play the game with java 7 since the game won't launch with java 8 and a vmparams modified. (Sorry if there are mistakes, English is not my native language)