that there were 9+ seats eligible for an upgrade
Either the agent initially made herself an error in searching for the upgrade booking class.
Or the system returned phantom availability to her.
9+ seats available in an upgrade class seems highly implausible to me. My guess is that the agent made the error and just quoted you the general availability in Business Class (all its fare classes).
You should have booked the Economy tickets with her (even if it costs more money). That way you could have gotten rid of these tickets more easily.
or those seats were all booked in that short amount of time.
That shows that she either didn't have a clue or lied to you.