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If they are small, it is likely a pollination issue. If they are larger, this is typically caused by under watering.

Since you do not want to fertilize seedlings until they have one or two sets of true leaves, as the fertilizer can burn the new roots, you should just make sure they are somewhat moist and have adequate light. After they get some true leaves, you can fertilize at half strength with a balanced fertilizer.

Black spots on pepper plants are often caused from an environmental disorder, in this case it's likely the hot, dry temps. Have they gotten sufficient water during this time? You can try adding some lime to the soil and then give the plants a good soaking. Also, mulch around the plants to help retain moisture. This is especially helpful when it gets hot and dry.

It sounds like your plants eiether got Fusarium or Verticillium wilt. While these are common to tomatoes, they can also affect peppers. Once it gets into a bed, it spreads to all plants in the bed. This article will explain more:
https://www.gardeningknowhow.com/edible/vegetables/pepper/pepper-wilt-on-plants.htm

There are a few reasons that this could be happening.

First, you may be removing most of the "hot" flesh when preparing the peppers. The veins and seeds inside the pepper are where most of the heat from the pepper come from. If these are too well removed, the pepper will be mild tasting in food.

Another possibility is that you have a jalapeno variety that is milder. These varieties are popular these days in the nurseries and you may have inadvertently purchased one of these.

Yet another possibility is that you are just being too nice to your peppers. The compounds in the pepper can become diluted if a pepper plant is too well watered and fertilized. You may want to look at stressing the plants just a little to increase heat.

It sounds like the plant may have blight. It mostly affects tomatoes, but can affect peppers as well. This article will explain more:
https://www.gardeningknowhow.com/edible/vegetables/tomato/early-blight-alternaria-tomato-leaf-spots-yellow-leaves.htm