Treatment: Increase aeration and circulation.  If the fish show acute poisoning, remove them to the benefit of an oxygen-rich tank (such as your quarantine tank).  Sometimes asphyxiated fish can be revived by holding it gently in a horizontal position, moving it slowly back and forth.  This causes water to flow into the mouth and out through the gills.  If the fish recovers, release it immediately to avoid additional stress.  Take care when handling puffers with the poison tetrodotoxin.

Background: Extreme levels of carbon dioxide in your tank will inhibit the puffer's ability to transport oxygen to its tissues, causing Hypoxia.  Hypoxia via carbon dioxide is likely during long transport, or in overstocked tanks.