Assuming you’ve hit the “Duplicate Certificate” limit (5 per week) and not the “Certificates per Registered Domain Limit” (50 per week), you might be able to evade the limit by including an additional subdomain on your certificate.
For example, if you’re trying to issue a certificate for:
example.orgwww.example.org
and it’s complaining about too many duplicate certificates, try changing your certificate request to be for:
example.orgwww.example.orgim-a-bad-boy.example.org
Of course, you’ll need to actually perform the validation process for the subdomain you add.