Probably you give the wrong data into the process of the CSR-generation. The FQDN of the Domain you want to protect needs to be filled in the CN-Field.
Assuming that you use linux and openssl and the domain you wanna get an SSL-Cert for is "www.mycooldomain.com" (SSL-Cert with www.):
$ openssl req -new -nodes -keyout mycooldomain_com.key -out mycooldomain_com.csr -newkey rsa:2048
Then you hit enter and have to fillout the required fields:
Generating a 2048 bit RSA private key
writing new private key to 'mycooldomain_com.key'
You are about to be asked to enter information that will be incorporated
into your certificate request.
What you are about to enter is what is called a Distinguished Name or a DN.
There are quite a few fields but you can leave some blank
For some fields there will be a default value,
If you enter '.', the field will be left blank.
Country Name (2 letter code) [AU]:CH
State or Province Name (full name) [Some-State]:Bern
Locality Name (eg, city) :Bern
Organization Name (eg, company) [Internet Widgits Pty Ltd]:Your Name / Company
Organizational Unit Name (eg, section) :
Common Name (eg, YOUR name) :www.mycooldomain.com
Email Address :firstname.lastname@example.org
Please enter the following 'extra' attributes
to be sent with your certificate request
A challenge password :
An optional company name :
Country for me is CH, my State is Bern, City Bern too, the name of You or your Company, Section is empty for me and then as Common Name, the FQDN you wanna protect.