Although difficult to be definitive on description alone, I believe the bugs are fungus gnats. They are probably not actually hurting your seedlings but their presence is an indication that you are probably overwatering, which will adversely affect most citrus in any stage.
Start by letting the surface of the soil dry. Adult insects can be vacuumed up or trapped in shallow plates/bowls/trays of soapy water or yellow sticky traps (or yellow plasticware coated with petroleum jelly). Once the soil surface is dry try sprinkling the surface with sharp sand or horti/agricultural grade (not pool filter) diatomaceous earth. Simple very dilute soap (not detergent) solution spray will be effective in killing them.
Watering with dilute cinnamon stick and chamomile tea will help kill fungi in soil that the gnat maggots live on.
Last edited by applestar
on Sun Feb 12, 2012 7:34 pm, edited 1 time in total.