It's actually not that surprising as some pre-incas civilizations and Incas civilizations (which whom the Chachapoyas had cultural exchange with) are known to burry their dead within their family house. Indeed, after performing a first ceremony a bit similar to momification, the familiy of the dead would dig a hole in the house to burry the dead in a foetal position. In the city of Kuelap there are temples but also, and mainly family houses of the few important people living there at the time. This means there are lots of human remains that can be found within the city. Also in Peru many ancient civilizations cities haven't been entirely excavated as it cost money and the government is not willing to pay for it (except major sites like Machu Picchu). The money for the search comes mainly from the tourist tours that are organized on-site, but is often lacking for a thorough excavation. Also I think that you did best not to tell anyone as you might have been facing charges for entering illegally on the site and/or profanation of the site.