Different orders are merged

I'm sorry, this is not core behavior, so you must have some module or Rules configuration working to combine line items into a single order this way. I don't know of any off the top of my head that do that, so you'll have to just research that in your own configuration. Sorry I can't be more help.

Hi
I am facing same problem

anybody please help me ...

My comment in #2 still applies.

I have solved this, by custom code.
First you create a login handler like.

function custom_module_form_alter(&$form, $form_state, $form_id) {
    
    if($form_id == 'commerce_checkout_form_checkout'){
        $form['buttons']['continue']['#submit'][2] = 'paypal_check_handler';
    }
}

function paypal_check_handler(&$form, $form_state){
    
    $order_number = $form_state['order']->order_number;
    $return = _get_current_stock($order_number);
    
    if($return['status']=='goto_paypal'){
      
     }else{   
       db_query("UPDATE commerce_order SET status = 'cart' where order_id='$order_number'");
       drupal_set_message("We are sorry - Following items are no longer available in stock after you added them in shopping cart. <br/>".'&ldquo; '.$return['product_name'].' &rdquo;');
       drupal_goto('cart');
    }
}

/**
 * This function check current stock.
 */
function _get_current_stock($order_id) {

    global $user;
    $order = commerce_cart_order_load($user->uid); // get user order details
    // get all product id of current order
    $results = db_query("SELECT cp.product_id AS product_id, cli.quantity AS order_qty,fcs.commerce_stock_value AS stock_qty FROM commerce_line_item AS cli LEFT JOIN commerce_product AS cp ON cli.line_item_label=cp.sku LEFT JOIN field_data_commerce_stock AS fcs ON cp.product_id=fcs.entity_id WHERE cli.order_id='$order_id' AND cli.type IN ('product','commerce_auction_lineitem') ")->fetchAll();
    $product_ids = $qty = $stock_qty = array();
    /*
     * @var $product_ids            : Product ID array.
     * @var $qty[$product_ids]      : get each Product order quantity.
     * @var $stock_qty[$product_ids]: get each Product stock quantity.
     */
    foreach($results As $value){
        if(!empty($value->product_id)){
            $product_ids[] = $value->product_id;
            $qty[$value->product_id] = (int)$value->order_qty;
            $stock_qty[$value->product_id] = (int)$value->stock_qty;
        }
    }
    // product id array convert in string forn sql.
    $product_ids_query = implode($product_ids, ',');
    /*
     * Here get product remaining stock
     * @stock   : Stock
     * @order   : Order qty in order table ( status is checkout_payment).
     * @avail   : available qty
     * @stock - @order = @avail
     */
    $results2 = db_query("SELECT cp.title AS product_name, cli.line_item_label AS line_item, cp.product_id AS product_id,cli.quantity AS order_qty, FORMAT(SUM(cli.quantity),0) total_order_qty,  FORMAT(fcs.commerce_stock_value,0) AS total_stock_qty, FORMAT((fcs.commerce_stock_value - SUM(cli.quantity)),0) As available_qty FROM commerce_line_item AS cli LEFT JOIN commerce_product AS cp ON cli.line_item_label=cp.sku LEFT JOIN field_data_commerce_stock AS fcs ON cp.product_id=fcs.entity_id LEFT JOIN commerce_order AS co ON co.order_id=cli.order_id WHERE co.`status`='checkout_payment' AND fcs.commerce_stock_value!=0 AND cp.product_id IN ($product_ids_query) GROUP BY cp.product_id")->fetchAll();
    $available_qty = array();
    foreach($results2 As $value2){
        $available_qty[$value2->product_id] = $value2->available_qty;
        $available_product_name[$value2->product_id] = $value2->product_name;
        
    }
    $redirection_var = array();
    $redirection_var['status'] = 'goto_paypal';
    foreach($product_ids AS $product_chk){
        if(!empty($available_qty[$product_chk])){
            $current_stock_qty = (int)$available_qty[$product_chk]; 
        } else {
            $current_stock_qty = (int)$stock_qty[$product_chk];
        }

        $ordered_qty = $qty[$product_chk];
        if($current_stock_qty > 0){
            // go to paypal
             $redirection_var;
        } else {
            $current_product_name = $available_product_name[$product_chk];
            $redirection_var['product_name'] = $current_product_name;
            $redirection_var['status'] = 'not_goto_paypal';
            return $redirection_var;
        }
    }
    return $redirection_var;
}

Thankyou :)