Have people ever challenged Hinduism?

Yes, very much so. Two religious movements, Jainism and Buddhism, arose from people realizing the flaws and inequality inherent in Hinduism (it is the basis of the Indian caste system). People also took issue with the cycle of reincarnation that dictated that you could, if you lived well (did not complain about your status), come back as a higher status until you were eventually reincarnated to the ruling class. Both Jainism and Buddhism focus on escaping the cycle of reincarnation, which is called samsara. Hope this helped.