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My wife received a 1099-NEC.

an NEC may be proper though a MISC wouldn't change things.   we can't say whether she should have been treated as an employee and taxes withheld or as an independent contractor. 

It listed the money she actually received, but did not list the money that was withheld for taxes. 

if taxes were withheld, a W-2 is what she should have received - not an NEC not an MISC. this is something she should try to straighten out with the company she worked for. that's what the IRS wants you to do before filing  - get the correct tax form.  however, if unsuccessful read the instructions at the top of form 4852 because the IRS want's to know about any misfiling. then you would submit your return with form 4852 to best estimate what the w-2 would actually be.

https://www.irs.gov/pub/irs-pdf/f4852.pdf 

 

 

warning if the IRS concludes she was actually an independent contractor, it will send you a bill. the withholding claimed on the 4852 will be disallowed. in addition, she'll owe self-employment taxes on her net income.  plus the penalties and interest.

 

consider if you want to handle this yourself or use a tax professional.