I would respond to the IRS with all of the information you have on the situation to help "prove" your case. I would go to your bank and obtain a copy of the deposited check, showing that you only received one.
I would also try to talk to both companies to see if one will issue a corrected Form 1099-MISC showing zero.
You can also try to work with the IRS' Taxpayer Advocate System. You can read more about that at this link here:
https://www.irs.gov/taxpayer-advocate
