Hi Amit
I assume you are talking about outbound deliveries. In this case it would be worth checking the customer master record for the receiving plant. In the sales area data there is a shipping tab which contains several settings used to control delivery creation for customers.
It is possible to control how the system behaves when you have a stock shortage and restrict the number of partial deliveries. This might help you control this situation and might be the cause.
Regards
Robyn