Sounds like it could be blossom end rot. Blossom end rot (BER) is the result of a lack of calcium in the the fruit. I personally use crushed egg shells sprinkled around the base of my seedlings to both keep soft bodied insects away from my seedlings and add calcium to the soil.

I do want to point out that BER does not necessarily imply a lack of calcium in the soil, but rather a lack of calcium uptake. This can be cause four situations.

1. Extreme fluctuations in water. (meaning you come home to find your plant bone dry and then give it lots of water)
2. Rapid plant growth early on followed by lots of dry weather. Fertilizers high in nitrogen can cause the rapid growth.
3. Overly damp soil. Good drainage is important.
4. Lots of soil salts. Watering will help remove the salts if that is the problem.

So if it is BER it comes down to watering and possibly too much nitrogen or not enough calcium. Watering is the easiest to figure out because you should know how much water you give the plants. A soil test should be done if you feel you are watering the appropriate amount.