When you click on recommendation rule to see group reused after every rerun, you will still see stale entries for older rerun. This does not affect the recommendation generated - just the additional context around reuse of groups.
SSP 5.0
The main cause for this is that the Postgresql DB table in which the reuse information is stored is not cleared for every rerun.
In the support bundle, look at the postgresql tables information for intelligence.recommendation_partial_reused_group table. You will see stale entries for previous rule ids from the previous start or rerun of recommendation.
Ideally customer should publish after a few reruns - so that the stale group reuse information does not clutter up the UI. If that is not possible, as a workaround - instead of rerun , customer can start a new recommendation with the same inputs as the current recommendation; The rule reuse information for the new recommendation will not have any entries from the previous recommendation.