i think its related to having the ships move at the end of the turn.
if a ship has ten movement points and is traveling to a point 5 spaces away you can hit the end of turn button since you have no idle ship's. the end of turn starts to process the ship moves and any extra movement points are lost.
the same if you have a ship traveling to an anomaly unless you manually controll it the ship stops its turn on the anamoly regardless of if it has 3,5 or 100 spaces left to travel.
i never realized that this would be applied to invasions before but that does put a damper on the game knowing that with only a slight bit of planning that ai pretty much cant win