The thing with Team Ico games, is they LOVE to leave the story open for viewer interpretation and theory making. There is NOTHING in the game that directly says the barrels are filled with the remains of those people or whatever.
My personal theory is that, before the valley master showed up, the valley used to be a pretty neat civilization that used the tricos as a means of defense- and were venerated guardians. You see trico statues in some prrts of the area- and the suits of armor have horns like the tricos. So perhaps actual people used to wear them. Now they've got shadow-y things animating them- similar to the shadow forcefield around the brain thing. The fact people had previously lived here may explain the presence of barrels scattered about.
Also, notice that the brain's tower looks VERY alien compared to the rest of the structures. Same goes for the weird glowing technology and gates that the armors try to drag you into. So I think the brain came in later, took control of the region, and began using the Tricos as a means to get food.
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