On such networks, certificate pinning is very common and possibly even recommended, contrary to the "Basic Requirements" and recommendations of CAs.
Failing to respect such deadlines causes penalties to the local governments, and in grave cases may even be a crime: "public service interruption" which would initiate a trial, with more fines and possibly jail time.
Thus Actalis had to choose between:
1. follow the CAs "Basic Requirements" that force CAs to quickly revoke certificates when a problem is discovered. Then most of the certificates would be revoked before the public customers managed to replace them - disrupting their operativity, risking penalties for the missed deadlines and possibly trial and jail time for "public service interruption". To avoid this, they would then need to demonstrate in a public trial that the public customers were well informed that certificates could be revoked and re-issued at any time with very short warning time, and they did everything they could to avoid the "public service interruption", both pre-emptively (when negotiating the sell of certificates and educating the customers) and re-actively (when the serial numbers vulnerability was discovered). Quite a hard path.
2. contact the customers, push them to quickly replace the compromised certificates, and revoke them only afterwards, thus avoiding service disruptions.
They chose 2. Unluckily italian public organizations are very slow, which in the end caused Actalis to miss their BR deadlines by a long shot.
And the defence against this stuff is curiosity - which is internal process. If you issue lots of certificates (say, more than a dozen) and you find that the "64-bit" integers in them actually only vary in 63 bits you ought to be suspicious. If Actalis (or other CAs) had declared "Hi, we found out about this after two weeks when we looked at our serial numbers more closely" instead of waiting for the problem with EJBCA to get called out explicitly I'd have _way_ more sympathy.
Likewise if you're sure you are implementing 3.2.2.4.6 Agreed‐Upon Change to Website, curiosity would suggest it's worth taking a look at some of those agreed upon changes and how they were verified, and how some failed. No failures at all? Well that's weird, let's look more closely - oh, we're counting 404 errors as success. Oops. (Yes a real public CA did this and in their case they did find it before someone else reported it).