After quick investigation i have found quick solution which work like a charm under Apache/2.4.10 (Debian 8).
1.Uninstall LetsEncrypt plugin
2. Modify file: /var/www/imscp/gui/plugins/LetsEncrypt/templates/LetsEncrypt.conf
3. Install plugin again
4. {APACHE_WWW_DIR}/LetsEncrypt/.well-known/acme-challenge - each directory in path LetsEncrypt/.well-known/acme-challenge should completely exists and www-data:www-data CHOWNed