The challan may be a delivery challan, hence it is the duty of the customer to verify the details mentioned in the challan to that of the physical delivery of the goods at his place.
After keeping a note of the deficient items that was not delivered as per the list of challan, he can inform the seller about it so that the seller will raise invoice accordingly.
If the customer is not verifying the details and the goods then the customer cannot blame the seller of the deficiency because anything can happen in the transit.
If the delivery boys played mischief between the shop and the destination and the customer not physically verifying the goods delivered then he cannot hold the seller responsible for the deficient items.
At least henceforth the customer has to keep a strict vigil over the issue.