Targeting change?

They do this with ships that have fleet attack boost modules.

I was unaware that fleet warp bubbles had the same effect. If I have access to fleet warp bubbles, I would either install fleet attack boost modules on those ships as well (to make it a command ship of sorts) designing it for a more defensive role, or build them as escort ships for my troop transport. Either way, I would expect those ships to be destroyed first givin their roles.

As for attack fleet warp bubbles, my guess is, they are trying to slow down your fleet since they could do so by destroying a single ship. Given that it makes sense to destroy a ship that has a fleet attack boost module to negate the bonuses it provides, attacking a ship because it has a fleet warp bubble sounds like a reasonable thing to do.

Obviously the fleet modules pose some threat to the enemy, but since they don't affect the attack/defense/hp of the carrying ship directly, there is a small fudge factor to boost their priority in the targeting list.

Well I built some warp bubble ships which haven't got any weapons at all and so far, they haven't been fired on first. Which makes sense really, unarmed ships that aren't giving an attack or defence boost aren't priority targets.

I use a "large" ship with warp bubble on it. I use it as a starship carrier to transport "tiny" fighters into battle faster. The ship has some defenses and weapons so its an attractive target. The tiny fighters however have no defenses but lots of weapons. The enemy attacks the carrier but then gets obliterated by my fighters.