That is a tough one. I would not want to gain a reputation as 'the guy that breeds stub tail ball pythons'.
Since you are certain this is an incubation issue and not a genetic defect - I would lower the price by 20% and never drop my price any lower. Why? Because lower than 20% would make it seem like you are tying to offload defective snakes. People may be more conducive to purchasing them as they grow larger and have a proven track record of health.
Just curious: Did you notice anything odd about the incubation? Did you use vermiculite as a media?