You say swarm, which means you used more then 1 ship, right? Then that value you got of your number of ships x their individual total defence doesn't matter. example:

You
Ship A
100 ships
500 attack each
1000 health each

Enemy
Ship B
1 ship
1200 attack
3000 health

So he attacks you, and does 1200 damage to your fleet Ship A. Since each ship has 1000 health, you lose 1 ship, but you still destroy his ship, as your combined attack is more then his 1 ships health (you do 5000 damage, but the ship only has 3000, so it shows 3000 damage done and he loses the ship). This is basically what happened. Your combined defence only matters if the whole fleet is destroyed. But you can still lose individual ships if an attack does more then their own total defense, not the combined total. Understand now?