The reason as to why skele-freak never evolved from anything and existed before skeletons were discovered:

Long answer: Skele-freak didn’t come from earth, but from a rather terrestrial reality.
Evolving 600 billion years ago, Skele-freak was the first type of bones in all of animation existence.

a different species then proceeded to evolve from skeletons, who ended up due to bone infections, reproduction, decomposition, and interaction with other species began to grow flesh, fat, muscles, etc.

Short answer: Evolved in a different universe.