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This happens because previous when you doing shopping from your store and add any product( suppose 1 book).then you didn\\\’t done checkout and leave this site...so that product will be in your cart...so when you will log in again that product will be in cart..
so now you came this site again and shop any product with 1 Qty(1 Pen) ..and go to checkout page and log in there...so this qty will added to previously added qty.(so now products in your cart will be 1 book and 1 pen)