Today I stuck with weird problem - links from site I expected to be indexed on Google, was indexed but not from that domain. Links were indexed by IP and other domain names I ran on my VPS. Something went wrong, terribly wrong:
By searching for one phrase, Google gaved back results on domains and IP, not the real URL.
The thing is, I have forced sometime ago exatly this domain to be the default, by using simple line in my ngnix server config.
listen 80 default;
This line made the domain name default for everything what was not specified. By now I removed this line from this domain and added to other. But actually it's smart to create a server config for default non-configured domain.