Can I include a letter to IRS with my federal submission explaining a discrepancy on a Form 1099-MISC that a Payer provided to me?

[ee-ea]

Yes, but you must file  on paper.

[Anonymous]

if you can tell us the reason for the discrepancy perhaps we can suggest a workaround.   the problem with submitting a letter with the return is that it may just get tossed without anyone at the IRS looking at it.  Mailed returns are not currently being processed so you will have a long wait to see what the IRS does.