They didn't lose the keys, a sub-CA did.
Which is to say, sub-CAs in itself are a giant loophole that needs plugging. Especially since AFAIK nobody is bothering with name constraints (RFC5280 section 4.2.1.10).
The reason nobody bothers with NCs is because they don't work very well in practice. They also have their own baroque matching rules that are not intuitive if you're from the land of UNIX globs.
(In fairness this is a self-fulfilling prophecy: a lot of validators handle NCs poorly or not at all, so there's no impetus to rely on them. But that's not something we can really save in the Web PKI's current state.)
The situation is even worse than I thought.
They hold intermediate certificates issued by TWO different root CAs, neither of which they operate.
So two separate entities didn't bother to read their certificate policy or inspect their operations. Have we not learned anything from past mistakes?
Roots should be responsible for all their sub-CAs, full stop. If they don't trust them enough to accept that responsibility, then the system is broken.
eMudhra is also a root CA operator. One root CA operator cross-signing another root CA operator is a good thing actually, and it's what allowed Let's Encrypt to work before their root certificate was widely trusted.
Issuing sub CAs to non-root operators has historically been a big loophole though it's not as bad these days since multiple root programs now require approval before CAs can do it.