Of course, you've had times where you and your boss didn't see eye to eye. Don't answer this question with a quick no, instead be honest and tell the interviewer a short story of a time you and your supervisor didn't agree with something.
"I have had a few times that my supervisor and I didn't see eye to eye on things but that's ok. They are in the leadership position and my role is to follow their lead. If the opportunity came up or I was asked my opinion I would give it."