What os was the target ?
Bsa uses its own yum.conf that’s generated on the fly. the /etc/yum.conf shouldn’t be read.
Are you using an exclude list in the job as well?
We are using the exclusions list in the PA job. We are aware that BSA uses its own yum.conf, however the odd behavior corrected itself after he reran the job making only that one change on the target server.
what three patches were 'extra' ?
?run the job in debug mode and gather the yum output and repo metadata that will be copied back to the appserver and attach or open a ticket.