You can fix the counts by running the following query in mongodb for each group that has the wrong member count.
// get number of users
db.objects.count({_key: "group:<replace_with_group_name>:members"});
// update group object
db.objects.update({_key: "group:<replace_with_group_name>"}, {$set: {"memberCount": <replace_with_value_from_previous_query>}});