It happens to me too under the same conditions.
Reproduction steps:
Send a standard ATTACK to a pirate without recyclers. (screenshot 1)
Send a standard RECYCLING mission with 5 small ships and 100 recyclers to the same pirate and let it arrive 2 minutes later. (screenshot 1) (make sure the battle is long enough)
-> "Aggression"- and "return after no more debris"-settings doesn't matter.
Wait for the attack fleet to arrive. -> fleet not seen on coordinates at all while fighting!!! (screenshot 2)
Wait for the recycling fleet to arrive. -> fleet is seen on coordinates. (screenshot 3)
Wait until the battle is over. -> Both fleets are seen on the coordinates. (screenshot 4)
The screenshots:
1) Initial condition:
http://prntscr.com/lr12kq2) After battle started (1 fleet arrived):
http://prntscr.com/lr15sn3) With both fleets arrived:
http://prntscr.com/lr18df4) Battle is over:
http://prntscr.com/lr19x1Result:
I have to guess that it's a problem with the standard attack mission because it has nothing to do with the recycling mission. The fleet doesn't show when the recycling mission is still underway.
Maybe only step 1 of reproduction is required - I just documented the full example which I tried and where it happened.