"followed IRS recommendations to file as soon as possible to avoid possible fraud from someone else filling under your name." - This is good advice.
It's unfortunate, but what's good for security (speed) is not necessarily good for accuracy. Ask anyone who shoots a rifle in the military.
At some point in the amendment process, you will be asked why you are amending your return. Answer something like there was a software problem with form 5329 such that the HSA excess contribution carryover was doubled, resulting in an excessive excise tax (the 6%) on the 5329 in Part VII.
Please see "How do I amend my federal tax return for this year?"
If you have any questions in the course of the amendment process, please come back to the Community.
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