I do not have this issue because Pa has 1 sales tax rate for an item. Now I do remember seeing links and Posts about testing for NY Sales tax. This might be because of what you are stating. I would call Square or Contact the Beta community to see if this is still happening. I do not know much about it since I am not in NY. Supports number is in my signature line below.
I have called several times and they said there is no solution to this at the moment. We ship all over New York and there are various tax rates. PA sounds much easier!
Square does not have a solution for this yet, but were asking for NY businesses to test a Beta feature about NY taxes. I mention this because I kept seeing the requests in this forum. So Square does not have it offically but may be testing this for in the future. So Square support would not have this feature for an answer if you ask about it but you may need to contact someone in Beta Testing.
I looked on the Beta page to see if there was currently a test for the NY Sales Tax, and did not see one. Here is a Link to the Beta Page : Beta-Community/ct-p/Beta-Seller-Community-Global
You might be able to inquire about it there.
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