T138102 revealed that there is stale project membership data from the previous structure at (for example) cn=tools,ou=projects,dc=wikimedia,dc=org while only the information at cn=project-tools,ou=groups,dc=wikimedia,dc=org is now being kept updated. To avoid confusion, stale data that is no longer being updated should be purged.
NB: (AFAIUI) the entry cn=tools,ou=projects,dc=wikimedia,dc=org contains information "as itself", just the members attribute is stale and should be removed. So any actual data purging should be double-checked by another pair of eyes.