Almost always, this is due to uploading files to the wrong place.
Your website will always need to be uploaded so that it's root directory (where the main index file is located) will need to be in the "www" directory. That's where the server will look for your index file, which is what tells the server where to find all of the other content of your site.
If you are using ftp software, you'll want to simply navigate to the "www" directory (or "public_html" - they are two names for the same directory) - and then you'd simply upload everything there, keeping the structure of your site in tact.
If you are using design software such Dreamweaver or the like, there will be a setting called something like "Host Directory" which you will simply set to "public_html"
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