Not enough information here but similar questions often arise when a self-employed person decides to start doing business as an S Corporation (including, as an LLC electing to be taxed as an S Corp) and fails to notify customers that they should now make payments, and issue 1099s if they feel the need, to the corporation and its new EIN.  

Are all the 1099s related to work done by the S Corp, showing income deposited to the S Corp account?  Is the S Corp owner reporting on his 1040 the income paid to him as W-2 income, and S Corp profits (whether or not distributed) as shown on a Schedule K-1?

Or is it another case of "I got halfway through setting up this new entity and it was confusing so I didn't finish" ?