The foundation of a hole punch cloud is traditionally a mid- or high-altitude cloud type such as cirrus or cirro-stratus. Such clouds generally form above 20,000 feet or so in the atmosphere. The National Weather Service has explained that such clouds are frequently composed of both ice crystals and super-cooled water droplets – water that is below the freezing temperature but still exists in liquid form. When such a delicate balance occurs, only a slight disruption of this delicate balance may lead to a striking result....(snip)...It is believed that a cloud may be disrupted in this manner when a a jet flies through the thin cloud layer. Such a disruption may spur the quick freezing of liquid droplets and evaporation of other droplets. This would create the void in the space in which the jet passed through the layer.
While the source of hole punch clouds may be somewhat uncertain, they are certain to cause quite a vigorous discussion.