Hello. Yes, Sometimes this happens. I have a few ideas as to why this happens...
It's called, Pythium Root Rot Fungus and it's spores are in the water and chlorine doesn't kill them.
The plant is fighting the infection in the root. The plant might heal in a few weeks or the fungus might win.
Next... If the interior of the seed get below 8% rh the seed might not sprout, because the energy sack (fatty acids), that is inside all seeds, has got too dry.
I recommend using RO water for all your sprouting. Start off by getting rid of as much fungus as possible. You'll have a better chance of full germination.
I also recommend a soak of 24 hours in RO water, 2 cups of water and 4 drops of 30% Hydrogen Peroxide. It helps clean the water.
As well as it softens the membrane so the seed doesn't have to work so hard to get out of it.
Then into the paper towel or straight into the sterilized soil, solo cup. A temp of around 100* f will kill most spores, so slightly steaming the soil will kill most fungus.
Hope that helps.
Try this one out... www.edrosenthal.com/the-guru-of-ganga-blog/how-to-professionally-germinate-cannabis-seeds
It's a really sterile procedure but it will give you a good idea.
Chuck.