You probably planted overly-mature seedlings that were too long in small pots before going into the ground. If they had flowers on them when you planted them, the plants would have remained stunted and produced low yields through the summer.
It could also be inadequate sun--bell peppers need a minimum of 6 hours of full sun a day, and 8-12 hours is better still. Incorrect watering--too much or too little--could also produce stunted plants. Finally, bell peppers are heavy feeders, and need a lot of organic matter incorporated into the soil before planting.
For more information on growing peppers, see
http://www.grow-it-organically.com/growing-peppers.html
Good luck!
It could also be inadequate sun--bell peppers need a minimum of 6 hours of full sun a day, and 8-12 hours is better still. Incorrect watering--too much or too little--could also produce stunted plants. Finally, bell peppers are heavy feeders, and need a lot of organic matter incorporated into the soil before planting.
For more information on growing peppers, see
http://www.grow-it-organically.com/growing-peppers.html
Good luck!