Yes, I've run into the same thing and lost a battle to it before I started to avoid doing that. Seems like the negotiator's Republic Determination ability which grants anakin's ship Undending Loyalty for 3 turns doesn't square with the description of Undending Loyalty:
Republic Determination
All allies have +25% Potency and Galactic Republic allies have +25% Accuracy. All enemies deal 25% less damage when attacking out of turn. Galactic Republic allies deal 10% more damage for each other ally with Valor, doubled for Jedi allies. If Anakin's Starfighter is present at the start of battle, it gains Unending Loyalty for 3 turns. Reinforcement Bonus: Reinforcements gain Critical Damage Up for 2 turns.
Unending Loyalty: Can't be defeated during the first enemy attack (including assists) that would otherwise defeat this ship. When reduced to 1% Health, gain Stealth and Protection Up (50%) for 2 turns and this buff expires.
It doesn't mention that Anakin's start-of-battle Undending Loyalty is undispellable, if that was the intention.