Railroad teir 1 tax is saying i paid to much in and i am owed a refund from my employer for the entire amount i paid in. How do i fix this?

Try adding an additional box 14 entry with the amount reported in box 1 using the drop-down code RR for Railroad Retirement Compensation. 

This should clear the error message.  

I have put in box 14

RR wages   $XXXX  Railroad Retirement compensation ($$ from box 1)

Tier 1          $XXX   Tier 1 Tax    

Tier 1 med  $xxx    

Tier 2           $xxx

Turbo tax still telling me employer over deducted.   Will this ever be fixed in turbo tax?   Should I do something else?

There are limits on how much your employer can withhold. See this website.

If you think your numbers are below these limits, please tell us what you have in boxes 3 and 5, and the actual amounts in box 14.

Until we see what you have, there is nothing to 'fix".

Railroad Tier 1 withholding is a higher rate than social security.   More withheld during employment = more paid out in retirement.    The withholding error on turbo tax is frustrating.    I wish you would fix your tables.