I am exporting an indesign file to a pdf. Ultimately I want a movie to only appear when I click a play button, otherwise it remains hidden. I placed the movie in a separate layer in indesign but it appears in both layers in layer mode in pdf. I want the movie to pop up only when someone wants to view it. I don't know how to address this since indesign is not exporting the layers properly
Interactive elements are not a part of the InDesign Layers. InDesign Layers and Acrobat Layers are a different thing.
AFAIK, InDesign not support popup video in PDF-export. But you can set this directly in acrobat pro.