Your 1099-R should have a zero in box 2a if it was supposed to go to a Traditional IRA and the same amount as box 1 if going to a Roth.
The check you deposited, if issued properly (often they are not), should have been payable to your Traditional IRA and the IRA trustee should never have deposited it in the the wrong type of IRA. Only the IRA trustee can correct their error.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**