FICA and MEDFICA were deducted from my income this fiscal year by error by employer. When I notified my employer they immediately notified the payroll agency and stopped deducting those taxes from the next paystub.
However, regarding claim they said they will just give me a letter saying that they would not be refunding this amount and I should claim directly from IRS as stated in instructions with Form 843.
Now, there was someone who said that getting those taxes from IRS sometimes takes a lot of time and is a big hassle and I might not even get it. Let me know how to proceed.
I think you got pretty clear instructions from your employer on how to proceed. File the form. You were very clear on that the employer will provide you with a letter that says that the employer is not going to refund you. That is the requirement for filing the form 843 in this case.