I'm using InDesign 2017, Mac Pro/Sierra.
I create multi-up templates for business cards. I have a business card master file for a client that has 5 different employees. I only show one employee and resave this file. When I place it into the business card template all the names show at the same time, one on top of another. Shouldn't the hidden layers in fact be hidden?
What filetype are you placing? What happens when the placed file is selected, and you click to Object > Object Layer Options?