The attack by Greymane happened at the beginning of Stormheim, which would most likely have been after the other zones from a story perspective and not at the beginning of Legion. By that point The Horde would have been working with key members of the Alliance, such as Malfurion and Tyrande, welcomed back into Dalaran by Khadgar, and mutually hunting the items assault the Tomb of Sargeras and prevent the Legion invasion. Nobody should have really believed The Horde and Alliance were at war. Even believing they were betrayed hinges on somewhat flimsy logic since 5 seconds after The Horde sound the horn Gul'dan and his entourage step through the portal and it becomes painfully clear that the whole thing was a Legion trap.

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Regardless, the Alliance side of that incident makes it very clear that Genn and Sky Admiral Rogers are planning to attack the ships regardless of Anduin's orders. It was a revenge attack, plain and simple. Possibly even an assassination attempt on Sylvanas. Rogers probably should have faced a court-martial, at the very least.