Is it correct to receive a 1099-MISC form when you were reimbursed for expenses you encurred on behalf of a non-profit? it seems odd that this was reported as income.

It is very common if amounts exceed $600 for the non-profit to issue a 1099-Misc.  You would enter that income under the "Income & Expenses" tab.  Go to the "Self-employment" topic and enter the 1099 information and the expenses. They should zero out, but theoretically you could have more expenses and show a loss.