Background: Internship in Ohio, USA with agreed upon stipend of $5,000 for the summer semester.

I'm missing $1,300 from my total stipend, before taxes. I've been told:

"My manager and I reviewed the information. Initially $500 was deducted to cover fringe benefits which is an expense the department has to pay for all employees. The remaining amount deducted was taxes, so there will not be any additional payments."

I didn't take any serious actions during the internship because I didn't want my supervisor to take it out on my grade for the internship but now I'm ready to take them to small claims court.

Could you please help me understand what my best course of action is?