Gross negligence, distrust eMudhra
Single-byte private keys, an off-script key ceremony, and re-signing CRLs with the bad keys when the good ones failed show a process failure severe enough that the CA shouldn't be trusted again.
CT doesn't protect non-browsers
Browsers enforce Certificate Transparency, so nothing went unnoticed there. But curl, pip, updaters and other clients don't check SCTs, so anyone holding the keys could quietly MITM them.
Revocation outside browsers is broken
Firefox, Chrome, Apple and Microsoft pushed blocks quickly through OneCRL-style lists. The rest of the ecosystem has little working revocation, and Firefox on Android was slow to pick up the block.