if you wondered what those mysterious human parts were near the end
"Dark, dark tunnels
Eli Roth: The underground tunnels that we reference in the film where priests and nuns used to meet and have sex and bury the babies if the nuns got pregnant are real.
It's something that's rarely spoken about in Chile, but apparently it happened in Spain too. We saw the tunnels but were not allowed access to film there, but there actually are tunnels filled with the dead babies. Nicolas told me about this while we were scouting Valparaiso and we incorporated it into the story."
http://www.gamesradar.com/exclusive-eli-roth-commentary-aftershock-behind-the-scenes-photos/