Same theme name issue with wordpress repository theme

WP checks for updates by sending data about all plugins and themes to the repository. To prevent false update messages for your own code you need to selectively scrub it out of those requests.

The example for theme by Mark Jaquith:

function cws_hidden_theme_12345( $r, $url ) {
    if ( 0 !== strpos( $url, 'http://api.wordpress.org/themes/update-check' ) )
        return $r; // Not a theme update request. Bail immediately.
    $themes = unserialize( $r['body']['themes'] );
    unset( $themes[ get_option( 'template' ) ] );
    unset( $themes[ get_option( 'stylesheet' ) ] );
    $r['body']['themes'] = serialize( $themes );
    return $r;
}

add_filter( 'http_request_args', 'cws_hidden_theme_12345', 5, 2 );

See excluding your plugin or theme from update checks for full post with details.