It's safe to say, since it's been proven these holes exist all over the Amazon, that they were created to catch or divert animals, to keep them from reaching their village. After finding the normal route of the animals and their crossings, the holes were possibly dug to confuse the animals and funnel them into the small foot traffic areas to be caught and killed - whether for food or to control their travel. If it would stop humans from wanting to traverse the land, animals wouldn't want to either. Also, I see "scientists" make this mistake over and over; the lay of the land now is not what it was back then, and large ravines that are there now may have been lush with greenery and completely flat. Earthquakes and landslides could have completely changed the overall landscape by now too.

"Hole soil analysis also found ancient pollens of maize – a key staple in the Andes – and reeds traditionally used for basket-making. In addition to this, there were traces of squash, amaranth, cotton, chili peppers and other crops that haven't been farmed on the arid land where Monte Sierpe sits. Because many of these plants produce little airborne pollen, it's unlikely they settled in the holes naturally."

Perhaps they dry best in these holes, the community built them together, like building an oven or kiln, the regularity and sections of 50 holes allow to track whose produce is where; and maybe you sell them on at the same time.

Or, how about ice collection - each hole gets filled with water/snow, it freezes, the lumps are the right size for carrying back to an ice hole. Maybe they can slide them down the slope like a historical ice-cube dispenser.