I think it may be a physiological disorder called catface, where the fruits become deformed due to some damage that take place at flowering stage. Though it is very difficult to tell the exact reasons, some research indicates it may occur due to following reasons.
1. Exposure of plant to cool/cold temperature three weeks before bloom may cause this deformity.
2. In some varieties particularly indeterminate type, this deformity happens due to heavy pruning of growing points which results in lesser auxin in plants.
3. It may happen due to pesticide damage especially 2, 4- D (a herbicide).
4. The sucking insect like thrips may also cause this type of deformities.
5. Also excess watering coupled with poor drainage may causes catface symptom.
http://edis.ifas.ufl.edu/hs200