I am not sure if this is an issue with the AI when using group move or if this is as intended ...
Group of ships about to jump, using a skill preventing one of the ships jumping stops all the ships jumping allowing the attacking ships time to destroy all of the ships.
Since the timer resets when the ships can jump again, you can effectively prevent the group of ships from jumping as long as antimatter holds out.
Now I'm wondering if this is a Micromanagement decision or if this is a problem...since to prevent this tactic, you can change from group move.