Looks like there’s a bug in our handling of domains with large numbers of valid authorizations: https://github.com/letsencrypt/boulder/issues/3576. We’ll fix it, thanks for flagging it!
You ran into this bug because you have 2,500 valid authorizations for one of your domains, which suggests that you are attempting issuance much too frequently. One common source of this problem with Certbot is the --renew-by-default or --force-renewal flag. I’d recommend you check your cron jobs for root, or your systemd units, to ensure you’re running Certbot no more than twice a day, and you don’t have those flags enabled. Thanks!