It's a little hard to say exactly what is causing this to happen.  It could be a virus or a bacterial infection.  Do you use clean soil and clean pots? Or do you reuse your soil?  If you reuse your soil, I recommend using freshly purchased soil, either a seed starting blend or a lightweight potting soil, and clean pots.  

But it could be caused by something as simple as overwatering.  The soil should be lightweight, not garden soil or topsoil, and should feel damp, like a squeezed out sponge. 

If you are watering properly and suspect a virus or bacteria is causing the seedlings to die, you can have a sample tested at the MSU Plant & Pest Diagnostic Lab: https://www.canr.msu.edu/pestid/ 

Thank you for your question.