All I can say is that you did something wrong. I just tried the process reporting $5,000 of income and reversing it as described and it worked fine with no net change in tax from before I started the process and no Self Employment Tax credit. If you're seeing Self Employment tax being created on the 1099-MISC issued in error it's clear to you entered the 1099-MISC, with an amount in Box 7, AS a 1099-MISC.
