So My W2 has the same amounts listed in box 1, 3 and 5. Box 14 says pretax and an amount. Shouldn't the amount in box 14 pretax be deducted from my Box 1 amount? If the answer would be box 1 would be the amount minus the pretax amount in box 14 then why is box 3 and 5 the same exact amount as box 1?
No, because Box 1 is gross taxable wages, not gross wages in total. The amount in box 14 has already been deducted from your total gross wages to arrive at Box 1.
but then shouldn't box 3 and 5 have that amount added back in?
No, not necessarily, because Boxes 3 and 5 are taxable amounts for Social Security and Medicare tax which may have the same exclusions. For example, medical insurance is not taxable for federal tax, Social Security or Medicare tax.
So if pretax dollars are listed in box 12 i.e. with letter D - 401k contributions - then why on that W2 is box 1 listed with this amount in 12 - with letter D subtracted but box 3 and 5 have that amount added back in. Is that because 401K contributions are taxed for SS and state?
Your first comment mentioned that Boxes 1, 3, and 5 were the same. Therefore, the gross wages (which isn't reported on your W-2) all have the same deductions. Pretax 401(k) contributions typically would be deducted from gross to arrive at Box 1, but not for 3 or 5. See: Retirement plan FAQs regarding contributions - Are retirement plan contributions subject to withholding for FICA, Medicare or federal income tax?
You should enter the amounts as they appear on your W-2 in TurboTax, and if you do not feel they are correct, I recommend that you inquire with your payroll department at work.
State taxes differ on 401(k) treatment.