It sounds like there may be an error on your W-2. If what you are saying is you have a W-2 that show $0 in box 2 but you are certain your employer withheld federal income taxes, there is an error on your W-2. For this, you will need to get in touch with your employer and request a corrected W-2.
There are other taxes withheld from your paychecks as well as federal income taxes - state taxes, social security taxes and medicare taxes are the main ones. Sometimes, these other taxes are withheld without federal income taxes being withheld. If you have your last pay stub, that would be a good place to look to see if federal income taxes were withheld.
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