My only issue with Trump's statement about a rock being a rifle is that it can be interpreted as him short-circuting the chain of command, and no military can function without a properly defined chain of command.
The military generals and people working in the Department of Defense all publically took issue with Trump's statement and denounced it.
Theoretically, a small kid could throw a rock, a soldier wastes him with his M-4, and could get off in military court on a technicality because Trump is the Commander in Chief, and this hypothetical soldier could claim that (s)he was following orders.
The reason why this situation is bad is because soldiers must have rules of engagement, and everyone has to be on the same sheet of music.
Trump interfered with this process, and it pissed off the military.