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If the seedlings aren't too rooted, you can definitely wash the soil off the roots and put them in new dirt. If they're too rooted and may cause too much trouble, you may have find some organic insecticide. Neem oil works. Unfortunately, that's where I stop. I haven't had any pest/disease problems yet (knock on wood).
Some pictures may help as well to ID the bugs.
You could cook the soil if you planned on using it again.
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