Federation Commander

If a drone is tractored in the Defensive Fire Phase is the drone counter moved out to an adjacent hex or is it left on top of the ship counter and moved along with the ship counter?

It is left on the ship card. It has been stopped *just* outside the ship's shields and therefore occupies the same hex as the ship.

This does mean that a drone tractored at one hex is treated differently from a drone tractored in Defensive Fire. A drone tractored at one hex is kept in that relative position to the ship, which means that when the ship turns, the drone will be facing a new shield. But, a drone tractored in Defensive Fire is effectively "glued" to the impact shield and will stay on that shield regardless of whether the ship turns or not.

Hope that helps!