Is it possible that you have multiple nodes running this software that are all using the same gateway? In the past, there have been issues like this because cloud systems/admins did not fully deactivate a node, and it's still running - and making requests (using up rate limits) without anyone realizing it. If the gateway is shared, they all contribute to the same IP limits, otherwise they overstep the account/domain limits.
There have also been issues with some employees of an organization installing new software and not telling others.
The 40/s rate limit is a combined limit against all the endpoints (acme + directory); it's enforced at ISRG's gateway.
It's possible that LetsEncrypt did change something. see Missing TLD [xn--4dbrk0ce / .ישראל] - #37 by mcpherrinm where LE noted they were doing some maintenance this week.