I'm able to consistently reproduce, even in 1.0.1.8 with Autosave 7
Instructions to warp fleet -
While paused:
1. Select Fleet 2
2. Change destination
3. Change destination again

It has happened with other fleets, but this is the most consistent method
Screen shots included.

1.0.1.6 - I have a fleet that's at a staging system before invading, I go to move it, and it teleports outside the galaxy for it's position.

Additionally, fuel tankers assigned to the fleet and set to auto do not fill ships and instead go back to what an unassigned ship does.