I've never seen my South American pufferfish puff under any circumstances, but the dog-faced puffer I looked after years ago would puff up if netted or otherwise stressed. So I think the likelihood of a pufferfish puffing varies quite a bit.
As you know, they do this when stressed. Provided they puff up underwater, there really shouldn't be any problems. It is only when they puff up with air that problems seem to occur. They have problems expelling air, and you need to intervene directly if the puffer 'gets stuck'. Otherwise, it can suffocate, because the air stops it keeping its gills under water.
On the other hand, if the fish is puffing up repeatedly, that might be a sign of stress or fear. I've never kept figure-8s, and can't really comment on the suitability or otherwise of a 3-foot aquarium for three specimens. But I'd certainly consider the possibility that one of the puffers is being attacked and feels threatened by the other fish in the tank. Look out for signs of fin damage, for example, and act accordingly.
Cheers,
Neale
