Why am I being taxed for non-taxable income?

I was on a contract job traveling full time for 6-months this year and the company paid me a $50k salary.

In addition, they provided $30/ day stipend for general expenses. 180 days x $30 = $5400

Last, they reimbursed me $3600 in total for expenses I incurred on their behalf after providing receipts.

=$9000 total for stipend + reimbursements

 

I received a W2 and 1099-MISC.  The W2 was as expected, but the 1099-MISC showed income of the $9000 in the "1. Rent" box.  

 

My understanding is that I wouldn't be taxed on this as it is not income, but reimbursement.  However, it substantially affects my refund when I input the 1099 info.  What am I missing?

Thank you!