I think you are right: it makes sense to use Perdo to generate worms from decaying flesh or plants (real worms, flies...), far less when generating them from fresh air or living plants like bees are. Why not Creo though?
Away from the book, but the upshot is that the worms naturally arise out of the substance- scorpians from sand, frogs from swampy water, bees from decaying vegetation. They are NOT produced from anything recognized as a seed- plant or animal. So they naturally, not quite spontaneuously, generate. However, in order to create them, you need a sufficient amount of the appropriate substance.
I figure there will be a lot of variations between games tweaking this. I'd certainly say you could use Creo to create them sans the appropriate substance as that becomes a non-naturally occurring creation.
As for Perdo, I understand the thinking generally, but I don't think it really applies here under 5th ed. Certainly decaying the substance is a worsening, but the creation of new life, even worms, from the decayed substance does not constitute a worsening of the substance itself. My 2 cents anyway.
Editted to add a very important NOT above.
So.. are bees made with CrHe, CrAn, or both? Can you make frogs with CrAq?
I guess you could consider them to be mundane examples of animals associated with Forms. IN the same way a flying dog can be Might 10 (auram), a frog can be a might-less animal with an association with Aquam. SO yes, I would allow the creation of frogs with Creo Aquam 
Sounds really cool and it is within the Paradigm
CHeers,
Xavi
Hi,
Yup! Nutritious frogs without vis. And spiders from thin air.
Mmm. Spiders.
Anyway,
Ken
Still away from the book, so I'm not sure whether the new way uses the Animal form or the elemental form for the Rego spell.
As for a Creo version, I'd go with Animal as the form. The whole point of the Creo version is you create the worm, still an animal, from nothing, as opposed to having it arise from the appropriate substance as it naturally can do.
Creo and Perdo can also be used to bring a target towards or away from its perfect Form. So a Perdo Animal spell could create maggots, and frogs too, I would imagine, come from foul water, so can be created with Perdo Aquam. Do scorpions come from spoiled sand?
I think that, though some worms arise from spoiled plant and animal material, the worms themselves are not a lesser form of the material. Checked A&A and and the effect of naturally creating worms from appropriate material is strict ReAn. And in RoP:M, under the beasts of virtue, strangely enough, bees arise from cattle bodies. Go figure.
And YR7, it's not to do with spoiled material. Scorpions simply arise from sand, dry earth. Just as toads and eels come from the river mud and mice come from wet earth. All of that is straight from A&A. The worms that arise from plants, animals, and even humans generally do so from the decayed vegetation or flesh, but there even some that do so while the subject is still alive, though definitely in a ill set of humors. Even so, the worms are separate beings from the subject.
Hmm? Someone mixed up their bees and wasps?