Why aren't some completed transactions reflecting in my order list?

Shopify Partner
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We are currently facing an issue where customers are trying the transaction multiple times. In this scenario certain transactions get cancelled while one odd transaction is successful but the order is not getting reflected in shopify. 
Ex.1.- As you can see from the screenshot attached the transaction for rs. 1365 has 3 attempts through 3 different sessions.
But the order id is same for the following 2 reference id and both have different status - customer email - 
Ref id - 1129XXXXX519 - Shipped - payment completed
Ref id - 1129XXXXX535 - initiated - Payment not completed
Request you to please look into this as the order has not been triggered in Shopify. 
Ex.2. - For following customer  customer tried doing the payment 3 times 
Ref Id - 112XXXXX1172 - initiated - payment not completed
Ref Id - 112XXXXX0415 - Shipped - Payment completed
In both the cases neither the actual order was generated on Shopify nor the Abandoned order was generated for payment failure. 
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