CAs are required to issue Certificate Practice Statements (CPS) which tell the world-at-large the parameters under which they issue certificates.
Here's the CPS for Let's Encrypt that was in effect when this problem was detected:
https://letsencrypt.org/documents/isrg-cps-v3.2/
These CPSs are used by the various browser/operating system developers to make decisions about which CAs should be included in their root trust stores; i.e. basically whether you're a CA accepted by "the internet".
Let's Encrypt's CPS said one thing (we issue certificates valid for 90 days), but their implementation did a different thing (issued certificates valid for 90 days + 1 second).
An inability to adhere to your CPS is a big deal - it is effectively an internal controls failure; and self-reporting of failures to adhere to your CPS is essential. The owners of the root trust stores are going to want to see seriousness from the CAs when it comes to adherence to their CPS, even in apparently de minimis cases.
e.g. refer to Mozilla's policy guide and its reliance on the CA CPS:
https://www.mozilla.org/en-US/about/governance/policies/secu...
No-one is suggesting that a one second difference in validity makes any difference in the real world, and Let's Encrypt has already uprev'd their CPS to make it clear that actually all they promise is that certificates will be valid "less than 100 days":