It sounds like you aren't talking about the Advent's Destra Crusader, which is their heavy cruiser.
If you are, I don't see how it could be causing the effect you are talking about.
If you aren't, then it sounds like either the Advent's Iconus with Repulsion that pushes enemy ships around, or the Vasari's Subverter which can temporarily disable ships. Try not to cluster your ships as that's when the enemy can be most effective.
You'll probably need to wait for more posts for good strategies dealing with those ships.