Line 64 on 1040 does not equal withheld taxes from W-2's. Did I enter incorrectly or is there other numbers included from 1099 or some other taxes already paid.

Line 64 Federal Income Tax Withheld 

Add the amounts shown as federal income tax withheld on your Forms W-2, W-2G, SSA-1099, K-1 and 1099-R.

If you had Additional Medicare Tax withheld, include the amount shown on Form 8959, line 24, in the total on line 64.