Good oral hygiene, still bad breath

So I have been texting this guy for a while who is my classmate. After a couple of days later, I bumped into him in the corridor, we had a good conversation. After a couple of conversations we had, I did notice he isn’t much okay to have a conversation with me. Later I notice that it maybe because of my bad breath. It’s a humiliation for me. How couldn’t I notice it? I told my mom regarding my bad breath, she contacted a hospital in Ajaxwhich provides family dentistry. So I went to the clinic and my doctor suggests me to brush twice and use mouthwash before sleep. But I do have good oral hygiene but still how can I have bad breath? What could be the reason for it? Is it a kind of bacteria that can be the problem?