After Transplanting Peppers Become Stagnant or Grow Very Slowly
The jalepenos do better, but the peppers are small and round. Bell peppers stay small and deformed.
Certified GKH Gardening Expert
Cool soil can do this to peppers and bells tend to be more affected by cool soil than hot peppers. Ideally, the soil (not the air) needs to be above 55F before you plant peppers. The warmer the soil, the better they grow. There are even some who believe that if peppers are exposed to temps under 50F, they will not produce well.
You may want to wait a bit longer in the future before putting them into the ground.
You can also try giving the plants some potassium and phosphorous. Soil lacking this can create stunted and deformed fruit as well.