Just in case somebody is using the Better WP Security plugin...
You can also get this problem if you turned on the "Hide Backend" feature, lost your admin cookie and are trying to go to http://mysite.com/wp-admin.
Go into your .htaccess file and you should see some lines like this:
RewriteRule ^hidden_login/?$ /wp-login.php?hyy864en85h3q03f5vfs2d [R,L]
RewriteRule ^.*wp-admin/?|^.*wp-login\.php not_found [L]
The second line shows you that wp-admin.php and wp-login.php are both redirecting to a page not found error page.
The first line shows what your alias is that you need to use to login to your site. So, the example above would mean instead of going here:
I would need to type:
And I would be redirected to the proper site.