Box 1 will be smaller than Box 3 when you have deductions that reduce your taxable income, for example contributions to your employer's retirement plan/401k. You can usually find an explanation of the amount subtracted listed in Box 12, with the explanation code.
Box 4 (Social security tax withheld) should be calculated on Box 3 (Social security wages). [TurboTax is correct.]
Please see this article on what to do if too much Social Security tax is withheld: Can I get a refund for excess Social Security tax withheld?
