We're not exactly sure, but we do know they're not from impacts.
They occur in a region of the planet called Tombaugh Regio, which has some of the youngest surface features on all of Pluto. The leading theory seems to be that the pits are caused by ice fracturing as the 'crust' of the planet is stressed by internal forces.
We still don't know for sure what's heating Pluto's interior, but one of the great discoveries from New Horizons is that Pluto is a very active world — possibly even as active as Earth's surface. Warm(ish) water in the interior likely behaves similarly to how magma behaves on Earth, leading to activity analogous to plate tectonics and volcanism.
...space Coyote?