I agree that you should have received both a 1099 and a W2 from your employer. They may be reluctant to do that because some people believe that could trigger an IRS audit. The reason is that independent contractor vs employee is supposed to be defined by your job function, not by your choice. If you were a contractor and then switched to be an employee without changing your job description, then the IRS could claim that you should have always been an employee the entire time, and so should every one of the other contractors that work for that company with a similar job function. It's a hornet's nest that the employer may not want to poke.
But that's not your problem; what should you do about it? When you say "he added my Federal and FICA W/H together", do you mean that total appears in box 4 of your 1099? If so, it sounds like the employer is expecting you to re-pay the employer portion of FICA. Can you ask them if they actually paid it? If they did, then I don't see them having a choice but to issue a W2, since the IRS would be expecting one. If they didn't pay your FICA, then the amount this will cost you is 7.65% of what would have been your W2 wages. IMHO it would be reasonable for you to request that they send you a check for that extra amount. Note: even though that amount will be less than $600 and you won't receive a 1099 in 2017 for it, legally you'll still have to pay tax on that amount so I think a good estimate would be to call it 10% instead. Depending on your personality and your relationship with the employer, if they choose not to "make you whole", you could threaten to fill out form SS-8.
Additional Info: (Thank you Bobson for bringing this up.) The situation you find yourself in is similar to the concept of "Contract-to-Hire". You start off as a contractor, and later convert to an employee. In order to avoid issuing a 1099 and W2 to the same person in a single tax year, companies typically utilize one of the following strategies:
- Bring the contractor in through another company (temp or staffing agency). This is commonly called corp-to-corp (C2C) and is the most common form of contract to hire arrangements, since it is legally very cut and dry. (Assuming the temp agency does their job, has the proper insurance, and pays the worker as a W2 employee, withholds the proper taxes, etc.)
- If the independent contractor would be issued a 1099 directly but is converted to W2 in the middle of the year, some companies will simply make the W2 status retroactive since the start of the contract (or the beginning of the year, whichever is later). This benefits the employee because no self employment tax will be due for the time they were a contractor for that tax year.
- Run the "contractor" through payroll right from the beginning (as a W2 employee). Companies typically don't like to do this because then they have to offer benefits too. It's possible that a small business that doesn't offer benefits would do this, and even though the person is referred to as a "contractor", they really are an employee from a tax perspective.
Your particular situation is closest to situation 2, but the reverse. Instead of retroactively calling you a W2 employee the entire time, your employer is cheating and attempting to classify you as a 1099 contractor the entire time. This is frowned upon by the IRS, as well as the employee since as you discovered it costs you more money in the form of employer FICA. From your description it sounds like your employer was trying to do you a favor and didn't quite follow through with it. What they should have done was never switch you to W2 in the first place (if you really should have been a contractor), or they should have done the conversion properly without stringing you along.