Upload multiple files in randomly generated folder using wp_upload_bits

Apply the following fixes (those with the // Fix <number>: comment) and your code would work in that only one random folder that will be created for all the uploads in the current session: ^{(Note: I presumed the $countfiles is properly defined in your actual code.)}

function file_upload_callback() {
    global $wpdb;
    $table_name="wp_order_quotes_real";

    $_filter = true;
    $randomFolder=""; // Fix 1: Define the variable.

    // Fix 2: Pass $randomFolder by reference to the closure below. That way, the
    // value won't be changed when the hook calls the closure the next time.
    add_filter( 'upload_dir', function( $arr ) use ( &$_filter, &$randomFolder ) {
        if ( $_filter ) {
            if ($randomFolder == '') {
                $randomFolder = ... your code;
            }
            $arr['path'] = $arr['basedir'].'/order-quotes/'.$randomFolder;
            // Note: I moved the `return` line to below.
        }
        return $arr; // Fix 3: ALWAYS return it!
    });
    //$_filter = false; // Fix 4: Don't disable it, yet.

    for($i=0; $i < $countfiles; $i++) {
        // Note: You should do this because the user may not necessariy upload the
        // files in sequence, i.e. file input two might be empty and the user only
        // selected a file for the first and third inputs..
        if ( empty( $_FILES['file']['tmp_name'][ $i ] ) ) {
            continue;
        }

        $upload = wp_upload_bits( ... your code here... );

    }
    $_filter = false; // Fix 5: Now you should disable the filter because all the
                      // uploads have completed.

    // ... the rest of your code here.
}

Additionally, instead of hardcoding the table name, you should do $table_name = $wpdb->prefix . 'order_quotes_real';. More importantly, please apply security measures like checking user capabilities and intent of the specific request.