"Certainly" is another word that you use to agree and disagree at the same time. The word "certainly" means "definitely". But it's often used to show a small feeling of disagreement or dissatisfaction. For example, if someone is acting a lot happier than usual, you can say:
You're certainly in a good mood today!
This sentence contains a very small suggestion that there's something strange about the person's good mood. Another example is:
I certainly hope he's able to finish in time.
Part of the meaning of this sentence is "I hope he's able to finish in time, although I don't think he will."