Before I discuss what is causing the allergies I have some interesting facts for you.
The prefix "hypo" means "less than" and thus the word hypoallergenic tells the kitten/cat buyer that the breeder believes the cat to to produce fewer allergens than other cats. How is this measured or regulated - well it isn't. There are no legal regulations defining allergens (let alone allergens in cats), nor are there any guidelines. So the world "hypoallergenic" has very little meaning.
Around 2-15% of the worlds population is allergic to cats and 1/3 of these have a cat in their home.
Up to 40% of Asthma sufferers are sensitive to cats.
A large proportion of cats surrendered to shelters are from allergic pet owners.