I notice that I am losing fat and gaining muscle while doing cardio (running 6.1 mph at a 1% incline). Why is this? I am already very lean (6'2", 9% bf male).
"Cardio" still requires more muscle use than a sedentary life style. Sure, it's not squatting heavy weights, and sure it's very high repetitions of the same movement.
But look at a competitive cyclist who doesn't do anything but ride: you will see incredibly powerful legs. Big vastus medialis muscles hanging by the knee that looks like they're smuggling avocados.
Your body will eventually compensate sufficiently to handle your running load and your muscle gain will flatline: distance running is well outside the effective bounds of hypertrophy (muscle mass increases). You'll gain enough to run, and that's it.
Be careful though about assigning any particular weight increases to water, fat, or muscle. I'll weigh myself once a month or so just for the heck of it. More important is my strength standards, conditioning, and performance in chosen athletic field.
Are you really 9% ? Here's one verification: http://www.builtlean.com/2012/09/24/body-fat-percentage-men-women/ Also you don't mention if you are also doing any other training besides the cardio. Are you? Note that training can increase water retention which would increase bodyweight without gaining fat, giving the impression of an increase in LBM.