There are civ-mil crises, and there are civ-mil crises. Intra-civ crises over how to govern the military can be civ-mil crises if the mil takes sides. So, if SecDef were a civilian like Gates or others, yes, this would count. That it is Mattis, who is really a general (sorry, recent retirement doesn't count for me, too much mindset is the same), yeah, this is a civ-mil crisis, because the top civilian has made a decisions that the generals are not implementing [conditional on whether the Trump orders actually contradict what Mattis is doing--I don't know the legalities of that]. When McMaster and Petraeus didn't do population centric counterinsurgency as Obama wanted, that was a crisis in civil-military relations, one that Gates bungled.
Of course, one qualifier: there is no consensus on what counts as a civ-mil crisis. Generally, the idea is that if the civs have preference A and mil has preference B, and then B happens, that is a crisis. But if civs have A and mil has B, and A is implemented, that's just the usual tensions that come with two distinct universes colliding.
To be clear, I believe we have been having a civ-mil crisis since Day 1 of the Trump administration because:
- the SecDef is a general;
- most of the usual civilians who play a role in national security are either non-existent (not appointed) or generals--recently retired or active (Flynn, McMaster);
- State as an alternative source of info/influence/agenda is gutted;
- Trump is an ignorant amateur who has no idea of proper way to handle civ-mil relations.
Bad news for the US, good news for those teaching/researching civ-mil. Oh, and what am I teaching this fall? Civ-mil!