You must be relative new to web hosting. There are two different "namespaces" involved. The file system is what you think of as files and directories ('folders'). The second one is url-path, which is part of a URL, that the web site deals with.
url-paths do not have to correspond to the filesystem. Think of them as pointers. If the web site doesn't consider a url-path to be a "special" pointer, it will attempt to look on the file system. And so if its not special and not on the file system, you get not found error.
The url-path '/stats' is one of these "special" pointers, a type called an Alias. It is aliased to the directory /home/username/logs/domain/stats.
The solution to your problem is on the Wiki at:
Making stats accessible with htaccess
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