Need to know exactly what's happening. Is it a wheezing sound, or a whistling sound? Can you "feel" (for lack of a better word) him wheezing? You said it only happened once or twice while handling. He could have been breathing heavily due to stress and may have whistled. I have a girl that whistled during handling from the time she was 100g to almost 400g, and nothing was wrong with her. Now that she is a bit larger, whatever shape in her nose/throat that was causing the whistle no longer does. If you don't see your snake breathing with its mouth open, or any mucus/bubbles around the nose and eyes, and if the whistle/wheeze is only happening during stressful moments like handling/feeding, it's probably nothing to be concerned with.

What are your temperatures looking like? Hot and cold side. What is your humidity at? What are you measuring those details with? How long have you had the snake? More details on husbandry and what exactly is going on with the snake will help us get a better picture.

That being said, none of us can diagnose your snake from a couple of sentences on a forum post, so if you think there may be something wrong, it would be best to get your animal to a vet.