When you gave the fleets the shift+click move to order, was that on the same turn that they reached the planet? There is an issue with shift+click fleets only moving together on the actual turn you give the order. Subsequent turns they will move as separate fleets. If they were more then one turn away from the planet when you gave the order that could be what caused it.
Not saying it's not a bug, it just might not be exactly a mine sweeping bug but more of a movement in general bug.
The whole shift+click move thing is a bit unreliable in general though. I am not totally convinced it works every time, even though I have tested it for combat and gotten good results at times. I have never tested it to see if it works for mineswpeeping.
In retrospect you probably should have had one more sweeper and then both fleets could have had 100+ sweeping capacity.
