Short answer from an expert:
This happened because root certs need to expire at some point. The root certificate that expired claimed to be issued in the year 2000 - that's older than pretty much every computer I currently use. It is unwisely to use such old things forever, because the security of the entire PKI/web depends on them. They need to be removed at some point, and September 30 2021 was this day.
Other CA's like GoDaddy simply use other root certificates, that don't expire this year - but they will some day. Maybe in 2022, maybe in 2030, maybe in 2040 - but they will at some point.
Since root certs expire, new root certs are issued to replace them. However, if systems do not get updates, they won't trust the new roots - now what do you do? This will inevitably break at some point, until the industry learns that not updating internet connected devices for 5+ years is not an option.
Let's Encrypts root certificate was accepted into root store programs roughly in 2016 - 5 years for software updates to distribute this certificate. For 5 years some systems were not updated, so it broke now.
In addition to that, Let's Encrypt decided to still serve a chain up to this (now expired) root certificate delibaretly. This fixed older Androids (those not having a new enough trust store - the update story again), but broke libraries with incorrect chain verification logic. This was a calculated risk Let's Encrypt decided to take, to help Android users. This issue can be mitigated by serving Let's Encrypts alternate chain, but it won't help systems without an updated trust store.
Looking at this thread, your issue apparently was that while you had the intention of serving reasonably up to date software, you actually weren't. These type of supply chain issues are hard to come by, I know that. I also want to point out that I don't intend to blame you or your company in any way. Rather I blame poor industry standards. You're not alone with these issues. I own a Smart TV by a well-known company that hasn't gotten an update to its root store since about 2012-2013, even though it is much more recent and has gotten software updates since then. Needlessly to say that it won't work with any LE site as of a certain day.