Ha? is equivalent to the English “Huh?” or “Hm?” but is used way more than in English and in more circumstances. It means “What did you just say?”, but it’s not rude at all. You say “ha?” when:

Sometimes foreigners think “ha?” sounds too aggressive, like the person saying it is being very rude or angry. That’s not the case at all, “ha?” is a very normal word that’s not rude at all, and it is used both between friends and in professional settings.