Seems to me that they all had the same angry face, it was more about the soldiers coming towards them, and she told him that they needed to talk after he told her that they had lost Magik/Juggernaut/Banshee (and she just knew that whoever wasn't there was lost) so it could be just about ending the whole thing.
I guess we will know what happens when the next issue comes out, a lot of us were sure that in the preview when Emma appeared it was Mystique because last we saw her Callahan had her secured and three idiots on the door doesn't really scream "secured" for an agency that has sentinels, but that was apparently what he did