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When the match rule is an auto rule, BMG runs internally which takes care of the transitive and redundant matches.
When the match rule is a manual rule, BMG does not run internally and hence the number of matches will be more.
PFB document URL and kb article that you can refer to.
Yes, this can happen because match job automatically calls the BMG (Build Match Group) process for auto matches found. The BMG process removes any transitive matches, thus elimininating any transitive/redundant match pairs found on auto match rules. So, counts can be less on auto rules as compared to manual rules.
Here's more information on what BMG is and when it is called:
The BMG process is not called for matches found on manual rules. So, that's the reason you'd see more matches on manual rules. There's an enhancement raised already (MDM-21416) to have an option to call BMG for manual rules too. This may be considered in a future version. You can track this enhancement through Informatica Network -> Change Request Tracking.
You can disable BMG (on auto matches) by modifying C_REPOS_TABLE's BMG_ON_MATCH_IND to 0 for the table you are running the match job on. By default, it is set to 1.