Issue with Domain and Sub-domain under the same hosting

Issue with Domain and Sub-domain under the same hosting

I have two websites:
Main Website www.WebsiteONE.com
Subdomain www.WebsiteTWO.com
They are both on the same hosting account. On the server, their files are
stored as follows:
..for www.WebsiteONE.com the files are stored in folder public_html/
..for www.WebsiteTWO.com the files are stored in folder
public_html/WebsiteTWO/
Now, i noticed that you can actually access WebsiteTWO by typing
www.WebsiteONE.com/WebsiteTWO/index.html (or any other file in the
WebsiteTWO folder)
Also i noticed that google indexes files from WebsiteTWO as being part of
the WebsiteONE
I don't want this to happen, is there anything i can do, maybe to the
.htaccess file. Or maybe you know another way. The thing is that these
sites are completely different and they have no connection with each
other. Still Google indexes files from site TWO to site ONE.