Sporadic known issues / Fluke. I've occasionally seen that. For me it occurs most often when toggling between factions in multi-faction games.
The issue is that occasionally when changing factions, loading saves, etc the system map fails to properly render active sensor contacts. If you then advance time the game processes the unrendered contacts as undetected and Bad Things happen.
To prevent that just double check that you can still see your targets after opening a save or changing faction and, if active targets are missing, refresh the system map or toggle between systems before advancing time.