The difference between the two factions is given down below with explanations for both.
Step-by-step explanation:
Gandhi and Hindus,
Majority in India
Hindus and Muslims living together
Jinnah and Muslims.
Minority in India
Separate Hindu and Muslim states
While mahatma Gandhi was looking to have India as a secular state with the people being free to live according to their religion be it Hindu or Muslim but that was not the case with Jinnah.
Both the leaders were also different in their leaning. While Gandhi as connected with the Congress he was rather apolitical and led the ideological foundation of the movement.
Jinnah was the leader of the Muslim league and was responsible for more fringe and area related movements but both were integral part of the freedom struggle.