Historically, Buddhism and Jainism were just some of the many sects or philosophical schools in ancient times. When was the separation of religions happened and when were all vedic and non-vedic sects clubbed under Hinduism?
Your starting premise that Jainism and Buddhism were just sects of Hinduism is incorrect. Any non-vedic philosophy is not a Hindu philosophy by definition. Therefore Buddhism and Jainism are not and were not sects of Hinduism or branches of Hindu philosophy.
Your confusion arises from the fact that they were founded by those born into the Hindu religion and borrowed heavily from Hinduism. Buddhism for e.g., has tantric portions taken from Hindu practices. Even their tantric deities mimic Hindu deities. Another reason for the confusion is from the style in which these religions chose to propogate themselves vis-a-vis abrahamic religions. The latter were historically more militant in their propaganda. You can look up crusades, and several citations in the Wikipedia page of Islam, one of them quoted below.
The expansion of the Muslim world involved various caliphates and empires, traders and conversion to Islam by missionary activities.
So the softer propagation of these religions and their advocacy of ahimsa which is a Hindu concept, could lead to confusing the religions are sects of Hinduism. They never were.
In conclusion, the Q is ill-considered and, therefore, incorrect and beside the point.
First you should understand that Hindu is not a religion. Hindu is a culture which followed by people from ancient India to few years back.
People write religion as Hindu in certificates and so on but it is false.
Hindu is a mixture of many religions like Vaishno, Shaiva, sastha, etc. Each religion has it's own god for example, shaiva has lord Shiva, vaishno has lord Vishnu, sastha has Lord Ayyappa, and so on.
It is a culture or a way of life. Buddha, Sikh, Jain, all are part of the Hindu Culture. The Muslim, Christian, etc., who follows the Indian culture is a part of Hinduism.
Neminatha (22nd Tirthankara of Jainism) is called close relative of Lord Krishna, hence Jainism was in practice even before Mahabharat.