Punch hole cloud formations are believed to occur when a plane or other object passes through a thin layer of clouds that contain supercooled water droplets. These droplets, whose temperature is below freezing although they are still liquid, are shocked by the passage of a plane, and suddenly freeze. They then fall out as snow, and may dissipate quickly, leaving an odd looking hole.
Here are some good examples, the first being shot recently near Myrtle Beach, South Carolina on January 7th, by Wesley Tyler, and showing an unusual multiple punch hole formation. The Myrtle Beach airport is only a few miles away.
Below is an image of the famous Moscow punch hole, whose picture went viral worldwide via the internet, and gave birth to all sorts of wild UFO theories.
Below is a punch hole near Sacramento, California, photographed around December 2nd. You can clearly see the falling frozen droplets coming down from the hole.