Well i have a site lets call it 12345.com and another domain and we'll call it 123.com Anyways rather then google indexing 12345.com it's doing 123.com/12345.com/ Is there anyway around this?
How is your hosting setup? Normally a website wouldn't be available as a folder of another site. If this is the case, the best bet is to create some sort of 301 redirect, to correct the url.
What a load of rubbish, you don't even know what the hosting environment is. You need to explain exactly how you have your hosting setup, two sites in one account? Seperate hosting accounts? both sites on ONE ip? You need to include much, much more details to get a resolution.