It's normal for Certbot to create a -0001 certificate if you create two different, partially overlapping certificates starting with the same name.
For example, if you run "certbot -d example.com -d example.net" and "certbot -d example.com -d example.org", Certbot would name them example.com and example.com-0001.
You have a bunch of different, partly overlapping certificates now. What outcome do you want, exactly?
You could edit your Apache configuration to use the www.my-domain-name.org certificate and delete the others.
You could also try to fix the issue that's preventing the mahara subdomain from renewing.
If you run "sudo certbot renew", what does it output?
I don't think so. 