Yes, that could happen when adding or removing domains to an existing certificate. You can avoid it specifying what is the cert name you want to use for your certificate so certbot will “overwrite” the existing certificate.
I mean, if you have a certificate for
example.com and now you want to replace it because you want to cover
www.example.com in the same cert, certbot will create a directory like
example.com-0001 containing the new cert but if you want to replace the existing certificate you should use the parameter
--cert-name example.com to specify the name of the dir where your cert should be located.
$ certbot-auto help all | grep -A 7 cert-name
--cert-name CERTNAME Certificate name to apply. This name is used by
Certbot for housekeeping and in file paths; it doesn't
affect the content of the certificate itself. To see
certificate names, run 'certbot certificates'. When
creating a new certificate, specifies the new
certificate's name. (default: the first provided
domain or the name of an existing certificate on your
system for the same domains)