If all your servers attempt to obtain a certificate for the exact same FQDN (
x.domain.com), these requests will run into the Duplicate Certificate rate limit (5 per week).
A way around that limit is to give every server an unique FQDN (e.g.,
serverN.domain.com), and make each server obtain a certificate with both the common FQDN (
x.domain.com) and the name which is unique to a particular server (
serverN.domain.com). If you do this, certificates for different servers would not be considered as duplicates; however, at the first issuance they will be subject to the Certificates per Registered Domain rate limit (50 per week). Once these certificates have been issued for the first time, however, subsequent renewals will not count against the Certificates per Registered Domain limit.
Obviously, each server must be able to validate its unique FQDN in addition to the common FQDN, but validating the server-specific FQDN may be much simpler (e.g.,
http-01 validation would need just a single
A record in DNS pointing to that server). Some solutions for validating the common FQDN were already given in other answers.