I see no reason to assume that the shuttle was travelling backwards. It is quite likely that the pilot was simply thrown faster.
If we base this on real world physics, this isn't actually that implausible:
The reason one might assume that the pilot would move backwards is that on earth we have air resistance, and so without a force constantly pushing forward, things slow down. This isn't the case in space. Depending on the nature of what the storm is made of, it is quite possible there is nothing to slow the pilot.
In more detail: while on the shuttle the pilot has the same velocity as the shuttle. In fact, without air resistance (it is space after all) or any other external force, the pilot would keep travelling at the same speed and direction as the shuttle if they let go. Whatever force that knocked the pilot off would only have to give the pilot a little extra acceleration forward to make the pilot move forward past the ship. Given the pilot is much lighter than the ship, they would receive a greater acceleration from the same force if applied to both them the shuttle.