I managed to get certbot working on my debian webserver which is running a bitnami django stack image. It worked initially however, I restarted apache to call the document root of the django files and now the certificate is returning not secure.
When looking at the details of the certificate in safari, the issuer is ‘example.com’ and no longer LetsEncrypt.
When I go to the apache2.conf file and check the SSLCertificate settings all the files point towards the letsencrypt folders but are clearly not being called.
How exactly did you install certbot? If you followed the debian instructions on certbot.eff.org you might have unintentionally installed a second copy of apache in addition to the one that bitnami provides, with its own separate configuration. Might you have restarted the wrong apache?