Is there anything in the Log window? This sounds like a possible alignment conflict, combined with an area-effect spell or attack gone wrong.
Did you by chance have the attacked character attack the thief by mistake? This can happen when enemies are locked in melee with a character, especially if Web or Entangle are involved, making it hard to tell whom you're targeting.
I did this once during the Palisades battle (attacked a Targos Guard instead of the enemy he was fighting), and all of the defenders then attacked me. Had to reload and refight the battle to fix it, since I didn't want to kill Olap and Company.
I can certainly see how a Neutral Evil thief might just take an accidental attack by a Lawful Good paladin as the last straw in their already tense relationship....
Hope this helps, sorry it's not better news
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