If you're talking about an application with the .app extension, then it's really not a file at all -- it's a folder that appears like a file in the Finder.
So, in essence, if you're trying to upload a .app extension "file," then you're really trying to upload a folder, which doesn't work with web-based upload forms.
One solution would be to compress the .app file as a .zip or a .sit, then upload that.