Robot ships were small automated ships which had specific uses.
The Blue Snake crime syndicate had a ship which was equipped with robot ships. They sent the ship into hyperspace to pursue the Bebop and it deployed robot ships to attack. The Swordfish II and Red Tail were able to be deployed as well, however, and were able to destroy them. The Bebop also used a sunstone to open a pocket in hyperspace, destroying more of them.
Robot ships have a resemblance to another set of ships in a chase scene from Asteroid Blues, but it isn't clear whether they are the same.