I think damping off is the biggest threat. When starting tomatoes or anything...give them plenty of air, warmth, and light to get them off to a good start. Bottom heat can help a lot to get all the seedlings up or most so you can remove any plastic tops etc. Air flow is crucial after they emerge. Keep the potting mix moist but not soaked. Don't put a fan directly on them but get that air moving around them.

The answer to your question greatly depends on the growing conditions you are providing. Inside or outside? You don't indicate your zone or location so you could easily be growing them outside as far as we know. Air and soil temps provided? Amount and type of light provided?

If they are outside then the exposure to the common pests and diseases increases 10 fold.

If they are inside then damp-off, soil molds, root rot from over-watering, and fungus gnats are the most common problems. Indoor seed starting is relatively pest and disease free IF proper air circulation, light, and water are provided. The most common problem is over-watering and that leads to all the other problems.

Dave

Here is a link that might be useful: How to grow tomatoes from seed.

Well thanks for the help!
-TomAndJerryGardener

The collar rot phase of early blight can effect seedlings. It would be present from contaminated seeds or grow materials (soil and maybe pots).

There are a number of other seed transmitted diseases that could show up from contaminated seeds.