Data breaches are considered "immutable", that is they are unable to be changed as they reflect an incident at a previous point in time. The only way to remove an email is for the owner of the address to use the opt-out feature and select the option to permanently remove the data from HIBP. This can only be done on a per-email address basis, one by one.
For more on why a domain may show more email addresses than expected, see Why does my domain show more email addresses than what could possibly exist?