The only reason it would charge shipping is if your shipping rules/modules are set such that shipping still applies to the order.

The email content you posted says something went wrong, but doesn't contain enough info to explain the cause. For that, you need to post the actual logs from the PayPal transaction: http://www.zen-cart.com/showthread.p...Logging-PayPal and once you've turned on the debug-logging (as explained at that link) then you'll need to recreate the problem by making the same purchase in your store.
So, while you're at it, prepare a click-by-click list of steps which can be used to consistently trigger the same problem every time, and post that along with the paypal logs for the transaction.