That actually wasn't a bug. They are designing the game so that all the systems on a ship and probably a station can take so much damage that they become completely inoperable. That is why every, at least every multi crew, ship is going to have repair drones.
Chris said this is something he wanted in the game early on.
Problem is they don't have them in the game yet, so they had no way to repair the engines on the retaliator.