A cleft palate is when the roof of the mouth doesn't close properly before birth, so the animal has a hole (cleft) in the bone of the roof of its mouth. This makes it very difficult to swallow. They can repair this with human babies, but puppies with the condition are almost always humanely put to sleep. :)
A cleft palate is where the two halves of the hard palate ( the roof of the mouth) do not fuse during the dogs development, which allows milk and food to pass out through the nostrils. The affected puppies usually have to be PTS as they cannot feed properly.
As far as I know there are many possible causes - recessive genes, or some form of stress to the bitch during the first 21 days of pregnancy. Stress such as infections, medication, live vaccines, accidents, poisoning, overheating ...