I don't know that the puffer would eat them (size issue), but he would definitely harass them. Dwarf puffers should be kept in a species tank with about 2.5-3 gallons of open water each. They are notorious fin nipper, and while some people say they keep them in a community tank successfully, the majority of people can't see it happening. At the very least, they shouldn't be kept in a crowded community tank. How many guppies are we talking in what size tank?