one question: the Pyre give Mana if you just build a ROAD there. could it be, that this is the reason why the AI does handle crystalized (e.g. already "warped") mana like it would get a bonus by just building a road there, even if he does not (because it only works with the Pyre, but maybe the AI regards the Pyre and the Crystalized mana the same, but on the Pyre he can't build an improvement, because it's blocked, while on a crystalized mana he can build an improvement, because it is not blocked).
ok. that sentence maybe is a bit strange.
Edit: a bit more structured
The Pyre gives Mana if you build a road there.
You don't need a node on the Pyre.
It's impossible to build cottages on the Pyre.
What if:
The AI regards Crystalized Mana as if it were a Pyre?
If so, then:
He would build a road there, thinking that building a road gives him the mana, which it does not (because this only works with Pyre improvements), but he does not know about that.
Because it is not the Pyre he can build cottages on the crystalized mana, and so he does it.
Maybe the AI just thinks a crystalized mana is like a special improvement which gives him mana just for a road. If this is the case, he should learn to regard them not like he regards the Pyre but like it regards normal mana (the blue one

).