Transfer of energy

I have a large ship that I'm testing shooting bullets at but I'm getting a small problem with it. I've calculated my best to get accurate mass and force for everything. My ship's mass is set to somewhere around 9 million and the bullets I'm shooting at it are set to 0.00395. I have set up a CCD skeleton with the ship and my bullets so that they can always collide. I know that it's better to use rays for bullets but eventually I'm going to be firing larger projectiles and i wanted to see how this panned out at first. When I create the bullets I just set their position and then give them a linear velocity of 800 in the direction they are going to travel. This all works and I get proper collision each time, no problem. What I don't like is that even though the mass of the ship is so great and the bullet is so small I still have these tiny bullets pushing the ship around. I have tried to set a material for the ship and bullets to modify the restitution and friction but it either doesn't seem to be working, or I'm doing it wrong. Also, the ship is sitting in water buoyant which seems mostly correct so I'm not sure if that is having any impact on my problem. Anyone have any ideas? I didn't find anything else related to this except for possibly restitution.

Thanks