The paid version lifts the limit on the total number of certificates the app will actively manage. Happy to provide a full refund if you have bought the license for the wrong reasons.
I think (guess) you are probably trying to request several certificates which are for subdomains of a main domain.
Let’s Encrypt is the certificate authority we use to generate certificates through the app. We cannot change those: https://letsencrypt.org/docs/rate-limits/
To process a refund please email support at certifytheweb.com
If this is happening with a set of domains that were already working ok then the renewal interval is probably too small. Go to Settings and set the renewal interval to 60 days to maximise the gap between renewal attempts. After 1 week you can retry the certificate renewal and the rate limit at Let’s Encrypt should be cleared.