The Scalqa leader wasn't actually dumb. He didn't reach that position through mere battle prowess, and his brain understood the weight of his responsibilities.
However, Khan and the humans were an odd race that didn't match what the leader was used to seeing. Their size was no indicator of their strength. They had access to strange flying tools, and Khan wielded mysterious powers that stretched beyond what eyes could see.
Actually, Khan was the strangest being the Scalqa leader had ever seen. The alien had been convinced of that since the attempted ambush in the forest. He had felt Khan's stare on him even from behind the trees, which surpassed what his mind could comprehend.
It was also odd how Khan had understood who the leader was before seeing the different attire. That small creature clearly had strange abilities, and the short battle further confirmed that point.