I'm trying to add a separate domain to one of my Google Apps account but I cannot find it anymore. I check in other accounts and it's the same. Only I can add a domain alias. Do you know if a issue or Google disable it?
It is still possible to add a separate domain to your existing Google Apps for Work subscription, but it is no longer possible to add separate domains for the Google Apps Free (Legacy) edition.
From their support page regarding the legacy edition:
The legacy free edition of Google Apps only supports domain aliases, not secondary domains.
The same support page also provides more details on the steps to take to add additional domains to your Google Apps for Work account, provided that you are a paying customer.