I was given a stipend for a training program that I was in, but when I put the miscellaneous 1099 into the system it goes in as self employment. I was not self employed so is there a different way to

The fact that you received a 1099-MISC means you earned money that was not part of a salaried job.  Technically, you were an independent contractor as far as the IRS is concerned.  You don't have to fill out the Schedule C.  Just put the amount on your return as "other income."