I'm not sure if Walter was subtly threatening Mike, Jesse or both of them. If he was threatening Mike then perhaps Walter was trying to show Jesse that Mike is overstepping his bounds just like Victor did when he decided to cook a batch of meth without consulting his boss. Walter is upset that Mike didn't tell him about the legacy costs and since Walter feels like he's the boss, he's taking this as an insult.
He might also be a bit paranoid and doesn't want Jesse to get any ideas about cooking for Mike and leaving him out. Therefore, reminding him that crossing the boss can lead to a painful ending, he's trying to make sure Jesse doesn't get too confident and comfortable in his new position of owner.
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