According Chrome's certificate transparency policy, all EV certs are required to be CT Qualified to be recognized as EV, and other certs may be required to be CT Qualified basically at their discretion. The example given is that, in response to a security incident at a CA, all certs from that CA may be required to be CT Qualified.
That seems to be slightly dated though, as you can see here in version 68 Chrome started requiring that all certificates issued after April 30, 2018 be CT Qualified.
Basically, due to concern about issues with CAs improperly issuing certificates (Google became quite upset about issues with Symantec when they found out Symantec had improperly issued a cert for www.google.com) Chrome now requires that all certificates be included in CT logs. This doesn't prevent mis-issuance, but it does allow it to be detected much easier.
When Chrome says that a certificate doesn't comply with its Certificate Transparency policy, it just means that it hasn't been included in the proper CT logs. Chrome is essentially trying to tell you "That's a valid certificate for the domain, but it's not in the CT logs, and due to past issues with certificates being mis-issued we don't want to vouch for its authenticity."