This is absolutely very, very unusual. Normally buns don’t vocalize like that – but they can cry out very very loudly when they are in motal fear. That’s a longer lasting, shrill cry though. It’s evolutionary “purpose” is for the predator to let go of the rabbit.
Rabbits’ vocalizations have to be interpreted in context. In some cases it’s clear what they mean, like rabbits that growl (and charge). In other cases, it’s less obvious what they mean. Some honk when they are happy (expecting a yummy treat f.ex) or make a little twittering sound when they eat or drink or groom themselves. They have the antatomical capacity for vocalizations, but most don’t use it much. It probably pays off to be mostly quiet in the wild.
If your rabbit seems fine while he’s making the noises, and he’s eating, drinking and pooping like he should and is normally active and has no symptoms of respiratory distress (such as sitting with his head tilted back or trying to breathe through his mouth), I can’t think of any illness that would present itself with whining. It seems you’ve ruled out obvious pain and severe fright. You could of course get him checked by your vet, if you have a bunny savvy vet.