Jinnah was not impressed by Rehmat Ali because he had an ideology that was fixated with a much larger Pakistan than was eventually created, and Rehmat Ali was critical in his views and used harsh language to express them.
In the end, Rehmat Ali was exiled and lived the rest of his days in England, and no-one was bothered about returning his body to Pakistan when he died.
The two men were critical to the founding of Pakistan (some say Rehmat Ali eve picked the name!), but they eventually fell out and he was refused back into Pakistan when he left the country.