That would be the best guess - overwatering - especially if in self watering containers. Seedlings shouldn't ever be left standing in water or prevented from drying out a bit as is only leads to root rot and nutrient uptake issues.

I'd suggest you post this over on the Growing Tomatoes forum here since they have their own forum and include all the info you can about the potting mix used and what if any fertilizer you have given them.

Dave