We were in South Carolina today & saw a hole in the clouds over the town of Lancaster. It was such a rare sight & strange feeling to watch this. We took a few pictures before it disappeared.
My research revealed per the Weather Channel:
These rare cloud formations, called "hole-punch clouds", develop in 
altocumulus cloud layers and are often the result of airplanes passing 
through the layer of clouds.
So, how does this happen?
The 
altocumulus cloud layer is composed of small water droplets that are 
below freezing called supercooled water droplets. If ice crystals can 
form in the layer of supercooled droplets, they will grow rapidly and 
shrink or possibly evaporate the droplets completely.
and National Geographic:
Clouds
 are made of water droplets, and hole punch clouds—also known as 
fallstreak hole clouds—occur when part of that cloud falls out, leaving 
behind a hole. That opening in the cloud is the result of an extremely 
localized snowfall.
 
Usually, atmospheric water droplets latch on to particles in order to
 form ice crystals, or snow. This happens on a massive scale during 
snowstorms. The only way water droplets can spontaneously form ice 
crystals without those particles is if temperatures fall to roughly 
-40°F (-40°C). (Learn more about these
 giant cloud holes.)
In a hole punch cloud, temperatures fall in only a small portion of 
the cloud, forming a localized snowstorm. When that snow falls, it 
leaves behind a hole. Refraction of sunlight by the ice crystals results
 in the rainbow, while the arrangement of those crystals gives us a 
bright patch of light in the middle called a sun dog. (See pictures of
 sun dogs and halos.)
The expansion of air as an airplane passes can also produce hole 
punch clouds by cooling water droplets enough for them to form ice 
crystals.