Hostgator addon domain names?

Hostgator addon domain names?
I have a hosting plan with Hostgator and I used the feature called addon domain name of this hosting plan. It means I can host many domain names on a hosting plan. What i am wondering if this will badly affect my websites in terms of SEO because people can get access to the content on the host from the different domain names. I've tried to make a search with the keyword of my website and see that Google indexed both my main domain name and the sub domain name where I pointed the main domain name to! Have you ever troubled with this and should I use this feature?
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