I have Ubuntu Server 16.04 but noticed that after setting up certbot and running certbot certificates I have some domains with more that one certificate e.g.
You need to make sure you’re not using those certificates, and that they’re the ones you want to delete, but yes, you can probably delete 2 of those certificates.
Check the list of hostnames carefully in each certificate carefully – this usually happens when you ask Certbot to create certificates with partially overlapping sets of hostnames.
You might have to issue a new certificate combining every hostname you still need and update your web server configuration before you can delete the others.