I assume the 1099-MISC forms are for work performed in 2016, and the expenses for this work was booked on your corporation's books and tax return. At this point you have no choice but to report the income on those forms on the corporation's tax return. Otherwise, your income and expenses will not match on either your personal return or the corporate return.
It's fair to say that the IRS will write to you later this year and attempt to put the $125,000 on your personal return. At that point you'll have to write back and explain the situation (this might be a good year to buy Audit Defense). Your only other option is to completely reconstruct your accounting to match the invoices and expenses with the 1099s and transfer those expenses to your personal return on Schedule C.
