Why is it saying that my employer withheld too much from my railroad retirement, showing the entire amount i put into it?

If you are getting a message about having paid too much railroad tier 1, then 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.  

If this is not your situation, please add more details about what you are seeing about filling out box 14 incorrectly.