Starting November 1, 2015 [1], you could no longer obtain certificates for "Reserved IP Addresses" [2] and any still in existence on October 1, 2016 had to be revoked.
Section 3.2.2.5 of the BRs indicate how one can demonstrate control over the IP address.
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1 - https://github.com/cabforum/documents/blob/master/docs/BR.md...
2 - https://www.iana.org/assignments/ipv4-address-space/ipv4-add...; http://www.iana.org/assignments/ipv6-address-space/ipv6-addr...
3 - https://github.com/cabforum/documents/blob/master/docs/BR.md...
(You might have been thinking about issuance for IP addresses in private/reserved IP space. That is indeed prohibited nowadays, just like "internal names", i.e. domains that don't end in a public suffix.)
There is a certificate extension - Certificate Subject Alternative Name that lists the following:
DNS Name: *.dns.cloudflare.com
DNS Name: dns.cloudflare.com
IP Address: 1.1.1.1
IP Address: 1.0.0.1
Most likely the extension was included as part of the certificate signing request.1 - Before Cloudflare I used to do this with OpenSSL and it requires half a dozen steps, but with cfssl you can do this quite easily: https://github.com/cloudflare/cfssl/wiki/Creating-a-new-CSR.