General confusion/discomfort:
* Disconcert: This is a good general word for making someone feel flustered or unsure.
* Unnerve: This implies making someone feel anxious or nervous.
* Perturb: This is a more formal word for disturbing someone's peace of mind.
* Fluster: This implies causing someone to become agitated or confused.
* Discombobulate: This is a more informal word for making someone feel disoriented or confused.
More specific meanings:
* Befuddle: To make someone confused or puzzled.
* Baffle: To make someone completely unable to understand something.
* Intimidate: To make someone feel fearful or apprehensive.
* Embarrass: To make someone feel ashamed or awkward.
* Disorient: To make someone lose their sense of direction or place.
The best word for your specific situation will depend on the context.