Wildcard labels in certificates are only valid for one level, which is the level they're on.
That is, a certificate for *.example.com is valid for a.example.com, b.example.com and so on, but not for sub.a.example.com. You would need a wildcard covering *.a.example.com. Note that the wildcard can only ever be the leftmost part in the DNS name.
It is also not valid for higher levels, that is *.example.com is not valid on the apex example.com or on the TLD .com (which is why you usually want to include both apex and the wildcard as an alternative name in the certificate).
This not a restriction by Let's Encrypt, but just the way how wildcards are currently specified/implemented in X.509 certificates/validators.
At this moment I'm not sure what your current question/problem really is. Without your actual domain name and/or a lot more information, I'm not sure how to help you at this moment.
A cert can hold up to 100 SAN entries.
[which can (all) be wildcard entries]
If you covered a name explicitly (without a wildcard) then, you should be able to do so now.
If you covered a name implicitly (with a wildcard) then, you should be able to do so now.
So...what has changed since October?