For a long time scientists believed hole punch clouds were caused by a plane's combustion. The latest research shows this is not always the case.
The first requirement to get a hole in the sky is the clouds have to be vertically thin.
These holes usually form beneath C-130 planes, the ones with propellers. Beneath the wings of these planes, temperatures are typically around 14 degrees warmer than the rest of the plane and surrounding environment.
If the environmental conditions with winds and humidity are just right, this temperature difference will create a dry punch of air falling from the sky that will evaporate the clouds beneath.
Thanks to Joseph McCown, Trinity, for the picture.