Get your taxes done using TurboTax

Can they issue a 1099 ... sure.   Is it right ... probably not.  What can you do about it ... file it as is should have been listed on a W-2 ... the TT program will walk you thru this in the 1099 entry section.  You will also need to paper file an SS-8 form with the IRS to report this "employer".   Or you can simply accept that part of your income is on the 1099 if you don't want to make a fuss.   If they did this to a lot of employees then you all need to report them so they learn a lesson.