Google indexing secondary domain as subdomain

[sgr2000]

I have a primary domain on my hosting account and several addon domains that I use as separate tlds. For some reason yesterday I am seeing the addon domains getting listed as a subdomain of the primary of the hosing account. For example:

I am using site1 as a primary hosting domain. It is not used. I have site2 as an addon domain on the hosting account, I use it as a stand alone site. Now I am seeing in the google index site2.site1 instead of site2. any way of coding the htaccess to not index like this

[lucy24]

Google can't index what it can't find. (For present purposes, "find" includes finding its name in robots.txt.) If

example2.com

is being indexed as

example2.com/example1 (sorry, mods, but you can see the problem!)

there has to be a reason for it to think this URL exists. To start with the most obvious: What happens if you try to follow these links?

You can't solve a problem through htaccess until you are absolutely sure what the problem is. Unless
:: cough-cough ::
the problem is that you need a way to test your custom 500 page. Been there. Done that.

[phranque]

you need to link internally to your canonical hostname.
you must also have hostname canonicalization redirects.