I'm not sure i think it can happen by an infection while the bitch is carrying the pups while they are developing. There's a lot of factors to take into consideration because some things aren't all down to genetics, plus it could be on the males side.
Warm regards Susan
If one of my girls produced a cleft pallet pup, then I personally wouldn't breed from her again, there is always that small risk it will happen again and I wouldn't like to be responsible for producing a poorly pup.