I received a notice from the IRS that I owe $3300 instead of them owing me $5000. I have checked all of the W2s and 1099s and all numbers are correct. What do I do.

What does the IRS letter say?  There should be a LT or CP number at the top.  Could be many things.  Do you get Social Security?  There was a problem with SS not showing as taxable on 1040 line 6b.  Check over your whole 1040 return.  Are the payments right?  Like withholding on line 25a and 1099 withholding on line 25b and estimated payments on line  26?  If you got any 1099R is the taxable amount right on 1040 line 4b or 5b?  

What does the IRS notice say is wrong in your tax return? Read the entire notice carefully. They might have made more than one change to your tax return.