Cannot seem to install my clutch properly?

I have been going back and forth with this Ford dealer who couldn't seem to install my clutch properly. After three attempts, the second two at no charge to me, the clutch seems to be working fine and the car seems to run okay. However, soon after I picked up my car the third time and drove to my destination. My check engine light comes on and stays on. When I turn my car off and back on it goes off, but will come back on and stay after driving some variable amount of time. Does a clutch replacement require any interaction with sensors or any component that affects the computers' readings that may cause the check engine light to come on?