Does she get a W2?  Or why are you asking?  If she is an employee and gets a W2 she will pay SS, Medicare & federal income tax and any state tax on her income.  They will take it out of her pay and it will be on the W2.  Paying into a pension plan doesn't change that.   The pension deduction is probably pre-tax which means it is not federal income tax now so it is excluded from the Gross Wages.  But it is not excluded from the Wages for Social Security and Medicare taxes.  

I guess I have bad intel then. I was told that with a pension she is excluded from receiving SS later.  If that were true why should she pay into it...

If she is going to receive SS later then cool.

Oh, I don't know anything about that.  Yes there are employers like govt or hospitals that don't pay into SS and have their own pension plan.  You have to ask the employer.  Just enter the W2 she gets.  See if there is anything in box 3 & 4 for SS.  

@dmertz  Can you explain it better then me?  Or who can?  

I agree - that is a question to ask her employer.    There are special rules for government agencies when  it comes so Social Security and they are all different depending on the agency and the job.

If payments are made to the pension and the employee is exempt from paying into SS then the W-2 will show that by virtue of boxes 3 & 4 being blank.