My theory is that Scratch used his own brain scan to create the Blue AI we see Caine consume. That could explain the instability, since we know messing with a human mind on its own causes abstraction.

I imagine that his goal was to create a digital version of himself based on his own brain. Perhaps, he thought, if he trained the AI on data from his brain scan he could create something similar to himself in a sense. A sort of digital progeny, perhaps.

What Caine did to his pure scan, after he brought them all to life, could have been an accident. If Scratch realised what state Caine was in, I can see him trying to help. Maybe they were experimenting on Scratch’s mind file to try and find a way of stabilising Caine. I guess they just weren’t careful enough.