I was hired and worked for a company as a employee. There was a brief period when the Co. had a lot of issues in accounting, they were not handling payroll correctly. An outside company handled payroll but the company I worked for also had the option of calling in and getting an employees deductions and issuing an in house check. The issue started when our Co. would call in and ask for the deductions but not specify to our payroll specialists that they in fact were going to do a in house check thus the payroll company not submitting the tax withholding. My payroll check was given to me with taxes taken out ,this happened twice and now they're sending me a w-2 & 1099. Can they do that? How can I fix this because I don't want this to affect my taxes. The amount on the 1099 is for $1000I would like to add that since I was misinformed by my tax preparer I went ahead and just submitted my tax refund on Friday after he told me it wouldn't make a difference including the 1099. I noticed it obviously does and would like to rectify the situation.