Jose and Martial are slowly building a give and take relationship. There's no doubt in my mind that Jose has not handled Martial very well in their time together, but Martial has had to change certain things of his game to succeed with Mourinho. He is making more runs, he's more energetic, but that's not really his natural game. There are players who are incredible game players but poor trainers or not running all over the place (not saying Martial is not solid in training, I honestly don't know), and I think the biggest fault of Mourinho is to have tried to treat Martial like he would any other player instead of being able to nurture the talent while slowly integrating his ideas into the player. When Sanchez came in, he didn't bench Martial immediately and tried to play them both but it didn't work and the fault with Jose only lies in that he gave up on Martial too quickly at that point when he was one of his most productive player prior to Sanchez arriving.
You are not going to get consistent performances from most players, especially younger ones, if from there one out you only play them sporadically. Now that he's getting a run of games, and that they're realizing for better or for worse they are stuck together, I think Jose is slowly adapting to Martial and vice-versa. At least that's my optimistic view on it.