The idea being that as the leader of the country the buck stops with him.

That the buck stops with him doesn’t make him personally responsible for every decision made by people under his command. If that was the case, it would be literally impossible to not be a criminal in any position of power - if GI Joe chooses to drive drunk on a Saturday night, that nets you a DUI. ‘The buck stops here’ means that the president must ultimately take responsibility for the decision-making that comes to his desk. It doesn’t mean “GI Joe’s DUI is your DUI”, it means “When GI Joe’s DUI comes to your desk, what you decide cannot be blamed on anyone else - this is your duty to make the big decisions and own up to what happens.”

In the Kunduz hospital strike, that meant a rare admission of guilt from the US government and reparations. If you think that’s not enough - then the buck stops with Obama. It’s his fault that more was not done in response to the incident. But the strike itself was not ordered or authorized by him, and can’t be reasonably blamed on him simply because he’s the CiC.