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Is your tracking option showing the center of the universe?
Since I have the same in 2 other mission groups. (Scourge of the Void: Capture the queen and Sublight Exploration Probes)
Both of these missions showing the center of the universe when tracking them.
This issue has been had by myself and a friend of mine as well. We think it's due to civilian/neutral ships being involved in the combat, then fleeing, which prevents credit for the kill going to your faction.