It's quite funny the intelligence oriented parellel minds are much smarter than the original Kumoko. They were getting majorly bothered by the queen seemingly doing nothing while her mind was being slowly eroded, yet the original Kumoko was just heedlessly wandering around looking for sweet fruits, not even noticing the bloody kilometers high pillar of magic energy shooting into the sky behind her.
Kumoko did note they haven't got much coordination between them. At that point it seemed likely the primary concern for the enemy was to prevent Kumoko from either teleporting or simply running to the middle layer. If the puppet had attacked more actively by jumping into the mix, I'd say there would have been a higher risk of Kumoko slipping past it to the middle layer. By staying back more and concentrating on observing, it could guard the entrance effectively. It's true it lessened the chances of actually killing Kumoko swiftly, but nonetheless, there was certain wisdom in its actions. The fact it did attack when Kumoko was rendered immobile seems to support my theory.