The detection process basically boils down to 'server admins need to check CT themselves'. A CA also doesn't have to be malicious; a non-CA malicious actor could also exploit a vulnerability in the verification process of an honest CA. Depending on the severity of the situation that's unlikely to get them removed from the root stores.
Interesting example: last year Cloudflare found out that a CA had been (incorrectly) issuing certs for 1.1.1.1. They only found out 1.5 years after the first cert had been issued. The CA didn't do it with malicious intent, and as far as I know they're still in business. https://blog.cloudflare.com/unauthorized-issuance-of-certifi...
Interesting example: last year Cloudflare found out that a CA had been (incorrectly) issuing certs for 1.1.1.1. They only found out 1.5 years after the first cert had been issued. The CA didn't do it with malicious intent, and as far as I know they're still in business. https://blog.cloudflare.com/unauthorized-issuance-of-certifi...