Why am I being taxed for non-taxable income?

[AdamM1]

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!

[JohnB5677]

A 1099-MISC form is a tax form that a business is required to issue to contractors and self-employed individuals who complete more than ​$600​ worth of work for the business in a year. If you work for yourself and receive one or more 1099 forms, you can claim expenses on Schedule C for those expenses.

However, you stated that you got a salary.  Did you get a W-2 associated with that income, or was it another 1099-NEC or 1099-MISC?

[AdamM1]

I received a W2 for my salary.

I received a 1099-MISC for my stipend & reimbursements.

I am self-employed (travel photographer) BUT I was on the official payroll as an employee for the 6-months I worked for the company.

[Mike9241]

I think your employer if you get a w-2 messed up by issuing the 1099.

Reimbursement for actual expenses is not taxable. snd is not reported on a 1099

expenses that are reimbursed simply based on the per diem rate, it is considered an accountable expense and is not taxable. again no 1099 should have been issued.  talk to your employer. there is nothing we can do.