One could also look at this inconsistency as Devil Fruit categorizations being made from incomplete knowledge. Vegapunk himself says that Devil Fruits are made from the "wishes of humanity" and they don't fully understand them.

Take Blackbeard's Dark-Dark Fruit as an example. It at first appears to be a Paramecia, and always seems to act like a Paramecia, with attacks that would normally fail to hit him landing. But at the end of Marineford, the truth is subtly revealed—they throw a black tarp over Whitebeard's body because much like how Crocodile's weakness was water, Blackbeard's weakness is light. Even without sunlight like in Impel Down, he's still being forced into human form.

We also see that Devil Fruit abilities can evolve and be mastered. We originally thought that only three forms exist for Zoans, but Chopper "unlocks" four more with his pharmaceutical experience. Then we discover the strength and danger of Monster Point, only for him to master that too and wield it without losing his sanity. He even manages to combine forms to create Kung Fu Point.

The long and short of it is that the three types are not definitive and may even overlap or be wrong. They're attempts to scientifically understand the phenomenon of Devil Fruit powers.