Consequences of late filing 1099?

[ILLMAS]

Not my client, but my associates'  client received an IRS notice stating they didn't report two 1099's, however they did report the income but the IRS adding it as additional income to a Sch C, I know this can be solved with a call or writing in to the IRS, but could this be the result of the issuer not submitting 1099's on time?  TP didn't receive a 1099 at all from the issuer.

[Lynn EA USTCP in Louisiana]

I have had clients receive similar notices when the income from the 1099 was reported but not in the spot on the tax return the IRS expected it to be.  Get a wage and income transcript to see if the income is reported in a box other than Box  7.