It is not likely that investment sales reflecting long-term gains could show in the short-term gain section of Schedule D without there being errant entries during the Form 1099-B entries. I suggest you review you investment sale entries and focus on the ones that list dates that reflect short-term sales of one year or less. There must be long-term sales entered incorrectly as short-term sales. If you find duplicate entries, you need to delete them.
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