I am attempting to cleanup web addresses and alter filename.php to filename/ everything works fine, however when I attempt to get it done inside a sub-directory it attempts to sign in parents directory for that file. What should i do?

    RewriteBase /    

    RewriteCond %{REQUEST_URI} "/favicon.ico" [OR]
    RewriteCond %{REQUEST_URI} "/js/" [OR]
    RewriteCond %{REQUEST_URI} "/images/" [OR]
    RewriteCond %{REQUEST_URI} "/inc/" [OR]
    RewriteCond %{REQUEST_URI} "/css/" 

    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ([A-Za-z0-9_\.\-]+)/$ /$1.php [QSA,L]

Your rewriterule does not match slashes, so it takes only the final segment from the URL. Give a slash and it'll match the whole request path. Or you might just matching against ^.*/$, if there is not some reason to not.