You hit the limit because you asked too many time the exact same certificate. But if - temporary - you create a certificate for two domains, the one you want and a useless subdomain, it will not be the exact same certificate... (but you will need to clean that after, for the renewal, in less than tree month!
You want a certificate for example.com. There is a limit of 5 identical certificate per 7 days: Rate Limits - Let's Encrypt so you have two options:
wait max 7 days
or, if you can't wait you can create a certificate for "example.com and anything.example.com" not two certificates, one, with both name in it. That certificate will work for example.com and will be different from the 5 certificates you already have created and lost. But It's better to wait if you can because you will need to be careful for the renewal of that certificate. Only use this solution if you absolutely need a certificate now and cant wait a few days.