By design, you cannot declare war on an ally. However, if you're allied to the last remaining faction, this should automatically trigger an alliance victory.
You can turn off the Alliance victory, and if mystic has done so it should not be possible for an alliance victory to trigger regardless of whether or not the ally is the only other empire remaining in the game.
mystic:
Is it possible that your 'ally' has recently picked up Negotiator I in the Neutral ideology tree? The one that makes it impossible to have wars declared upon you for 50 turns?
