Chances are good that you have Damping Off Disease. This is a fungus related disease that causes seedlings to wilt and die overnight.
There are many funguses and root rots that can cause damping off. If you have fungus gnats flying around your plants, you probably have a fungus as well even if you can't see it. This fungus lives on the soil and creates havoc in your seedling beds.
Babies can be affected even before they break their seedcoat. Moisture from the fungus ridden soil enters into the seed and your plant is already doomed. In this case, you may not even have a seedling at all. It could rot under the soil before emerging. If you plant a ton of seeds and only get a few babies, then they probably fell to the fungus in the soil.
Sometimes you have a young plant or even a maturing plant that looks stunted or loses it's leaves early on. All signs of damping off later on in the plant's cycle.
Prevention is everything to get a great garden. First, make sure you purchase disease free seeds. Soak seeds for 15 minutes in a bleach concoction containing 1 quart of water and 1 teaspoon of bleach. Plant immediately. Use sterile soil. If you can solarize your garden, do so to kill any fungus or other diseases that may be present in your soil. Maintain soil pH. Get a pH meter and keep an eye on the level of alkalinity. As you keep watering, acid is leached out of the soil so you end up with more alkaline soils. You want to maintain a balance of 6.2 - 6.5 pH.
When planting seeds, place seeds on your soil. Then cover with a medium less susceptible to fungus such as milled sphagnum moss, chick grit, or course sand.
Mist plants with an antifungal concoction such as clove tea, chamomile tea, light dusting of cinnamon (only once), fermented stinging nettle tea, powdered charcoal (only once), or a milk spray (1 gallon water, 1 cup powdered milk). Milk really works but no one seems to know why. Studies have shown the benefits of using milk for other problems such as mildew. (http//147.46.94.112-journal-sej-full-c12_199908_180801.pdf)
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