If employees had it set up that employer withholds taxes and there was a mess up can employer deduct from employees check for the amount the employer didn't withhold?

[chelseadm16]

Employer messed up withholding taxes and took over 400 from employee. Even though it was employers job to withhold taxes. Shouldn't it be employers out of pocket expenses that cover their mess up?

[VolvoGirl]

You will get credit for all the federal and state withholding actually taken out.  Wait for your W2.  

You don't get back any Social Security or Medicare (FICA) taken out.

[Critter-3]

Sounds like they made a mistake and under withheld at some point and they eventually corrected the error ... it may have stung but it was the correct thing to do.  

[Opus 17]

I don't quite understand your question.

You are responsible for 6.2% social security and 1.45% medicare tax.  If that wasn't taken out, it is absolutely a tax you owe and the employer must withhold it from your pay so that you have paid the correct amount by the end of the year.  And it doesn't come back as a refund, that is your tax you owe.

If the employer withheld too much or too little state or federal income tax, that gets worked out on your tax returns at the end of the year.  If the employer withheld too little at the beginning of the year, and then fixed their issue and started withholding the normal amount, it is more or less optional if they want to over-withhold to catch up.  If they under-withheld, you might owe tax and a penalty when you file your return.  If they over-withhold, you get any extra back as part of your tax refund.