The travel reimbursement was probably pretax so somehow tax has to be paid on it.  The answer is that you have to treat it as self employment income and pay those taxes. 

If the company did not do it on a pre-tax basis (which is stupid of them), it should have been added to your W-2.

Enter "8919" in the search box in the program and it should take you to the section to deal with that.

As a side note, you may want to tell the owners or executives in that business that they will save money if they find a better accounting department that knows taxes better.