Unusual behavior of Shopping Cart (Drupal Commerce)
What you describe is the default behavior in Drupal Commerce, as it is supporting the idea of "multiple carts", so when you log in you get the items that you've got in your current cart and the other cart will be kept in the "background". 

In fact, if you end the purchase you have once logged in, you'll most probably see that the items you had in the cart in the first place are back in there.

I'm afraid this is something you can't solve without some coding or rules, the theory here is that on the user login event, you get all the past orders from that user and combine them in the current cart of the user. This is not something you normally want as the cart pulled might be old.