I have not found this on forums:
When moving ship (by right-clicking) quite often it happens the ship moves less then it's available speed allows.
So when moving ship which has speed 5 it moves only 4 grid tiles, and then reports it has 0 available movement points left.
The movement don't have to be continous, ie. I can move ship 4 tiles first, then I try to use 1 last mp and the ship does not move (at best it turns to face the new direction), but the point is spent.
Not sure if this happens only when speed bonus is chosen, but it may be connected to this.