They knew that messing with Chaos, Order, and divinity was dangerous. They knew that from personal and clear experience so they were very careful in their fusion. They didn't bring Chaos energy or the divine energy of order into the fusion at all so as not to recreate the terrible events that almost killed them.
Their carefulness was fruitful and they even succeeded in creating a functional world engine. Unfortunately, there was something they didn't count for in this fusion. They didn't account for the sparks of power and what they would do when presented with Chaos, Order, and divinity.
It is not their fault that they ignored the shards of power. After all, Legion-5 might as well not have one. It hasn't done anything to him or affected him in any way so they overlooked it.
They knew that their sparks of power were there but they didn't think the two black orbs would affect the fusion. They were wrong.
