Best solution for now (by vege.net but rewrited a bit by me):
1. cd /usr/share/ca-certificates/mozilla/
3. mv lets-encrypt-r3.pem lets-encrypt-r3.crt
4. dpkg-reconfigure ca-certificates
In this step check new letsencrypt Cert (lets-encrypt-r3.crt)
5. Edit file: /var/www/imscp/engine/PerlLib/iMSCP/OpenSSL.pm and comment line 134 with # to look like that:
6. Go to Let's Encrypt tab on your domains and press button to renew certificate.