The 1099's that were filed were 1099-misc, however on the 1096 form the 1099-s form was checked instead of the 1099-misc. How can I fix this if I have already sent the forms to the irs?

The 1096 is like a cover sheet -- it is submitted solely to list the variety of forms that will be filed with it. If you forgot to file any of these forms or made a mistake on one of them, you need to file a new 1096. Make the corrections as soon as possible to avoid penalties.
For Incorrect money amount(s), code, or checkbox,
you need to prepare a new transmittal Form 1096.and Provide all requested information .File Form 1096 and Copy A of the return with the appropriate service center.Do not include a copy of the original return that was filed incorrectly.