Place some fine netting/pantyhose over the filter intake (what make of filter is it?)...
My filters a hvdor interpet ipf4 duo whatever that means?
Those filters are good for up to a 4 foot tank. How big is your tank? If it's a lot smaller then it could be just too strong and you might want a smaller filter.
They do have a flow control thingie on them though so you could try turning it down to the lowest setting and see if it helps.
Some fish are just too curious and will always get themselves stuck! I've lost 5 of my 7 pygmy corys to their own nosiness and one of my gouramis (tried to swim behind the filter, turned itself upside down and then got stuck behind the sucker and couldn't free itself). You do have to worry about their mental agility sometimes!
Don't know very much about puffers I'm afraid, but they will get more aggressive towards each other as they get older. Should ask in the oddballs section for more advice.