Your description would imply that some of the discovery filters (the 'machine' listings within the machine group) either resolve to some of the same machines (e.g. there are multiple entries which point to the same machines), or there are entries which are set to 'exclude'.
It appears that in the Operations Monitor when it says Close (scan complete) its not really complete yet. If I look at the results at the scan I will see "Warning: Scan still running - incomplete results" after some time the machines will appear in there.
This is happening to us as well and has never happened before. I just performed a scan on 61 machines. As the scan ran, Operations Monitor showed "61 of 61 machines complete" and that it was still running, however only 3 machines were showing in the preview section below.
As time went on, the Scan Summary page showed up to 12 machines total scanned while also saying "scan still running - incomplete results". I went back into Operations monitor to see that it now said 12 of 12 machines complete, close scan because the scan was complete.
How is that possible? I've just now checked 30 minutes later and the Scan Summary page is up to 29 machines scanned now. That's incredibly slow compared to the way things used to run. We've been running version 8.0.2 for a long time and never had this issue.
Any ideas on what may be causing these scans to report incorrectly in Operations monitor, and take a much longer time to finish?