I have read other similar discussions, and there seem to be two schools of thought:
1) Enter it as negative "other income" with an explanation. However, I don't see how to do this. (You can go to "Enter Business Income That's Not on a 1099-Misc" and enter a negative amount under "Other Income"--but there is no place to enter an explanation.)
2) Enter it under "Business Expenses Not Yet Reported" (on TurboTax) or "Other Expenses" (on Schedule C) with an explanation.
Here's something that might or might not help:
The detail information you enter about all the 1099-MISCs you receive is not included in the income tax return you send to the IRS. All the IRS sees is a lump sum of "Gross receipts or sales" on line 1 of Schedule C. If you have multiple 1099-MISCs you've entered, and perhaps some revenue not reported on a 1099-MISC, the IRS just has no visibility to the fact that you've entered a dollar amount that's less than the amount on this particular 1099-MISC.
So if you have multiple revenue sources beyond this one 1099-MISC I'd say "make a note on the 1099-MISC of exactly why you used a different number on your TurboTax entry than the one shown on the 1099-MISC and save that 1099 - along with all your other 1099's - with your paper copy of your 'as filed' income tax return." Your only obligation as a taxpayer is to report your income correctly, not blindly enter incorrect information that's contained on a 1099-MISC.
If this 1099-MISC is your only revenue source then you can do exactly the same thing - enter the correct number, not the one printed on the 1099-MISC. If the IRS ever comes calling you explain the situation and that should be the end of it because you've reported your income correctly. If you don't want to do this, and I assume this is Schedule C income, then make up an expense that gets your net business income correctly stated. What you call it is your choice since it's highly unlikely that any person will actually read what you entered.