When clicking on chickens with nether wart it will cause the chickens to breed

I can confirm in both 1.5.2 and 13w22a

Why is this intended?

Because Nether Wart is considered a seed, and all seeds (wheat, melon, pumpkin, nether wart) can be used to breed chickens.

Does that mean not being able to bone meal nether warts is a bug?

Probably not. Nether Wart only grows on soul sand, and doesn't care about light. It's an unusual plant. It doesn't benefit from whatever nutrients are present in bone meal.

This has been fixed