The Event Phase instructions for Waves 2 and 3 state the incorrect hexes that the AI should construct its spires on. It should say:
"Construct a portal spire – [fortification, fortification] on each Hex C and a refractor spire – [attack, range, attack] on each Hex D, if possible."
The AI is rebuilding its portals and refractors on the same hexes that they had them on during setup.