If you are selling stored codes, the list you paste in only gets saved when you click Submit to save changes and proceed to the button codes screen, so any codes sold before you click Submit would only be from codes you had already pasted in for that product previously (not including any new codes you were adding).
I think if you use the button to "Go back and make more changes", that remembers the settings you had just added rather than re-reading them from the database. In that case, any new codes you had just Submitted which got sold after clicking Submit, but before you went back to make more changes, could be resaved to the list.
To avoid this, simply avoid using the "Go back and make more changes" button for Stored Codes products. Instead, click the Seller Admin link in blue, under the Sellers tab near the top of our site, then from there, you can to to View/Edit Products, select the product and click Edit to start editing it with its current settings and codes.