The Subject Alternative Name field in the certificate must list both. Maybe the CSR wasn't properly created to include them?
This is an image from a GoDaddy cert just like the one you got:
Check to see if both entries are there
I purchased a single-domain SSL from GoDaddy. It was confirmed to me via their support that this certificate covers both the bare domain, AND the www. subdomain.
When I attempt to add the "www.domain.com" Custom Domain in my Azure Container App, it shows "No certificates match the selected hostname". I am able to add the naked domain without any issues.