I am trying to export print files from a large template file. Why are my layers showing up in the PNG and how can I get it to stop? Exporting to screens does not help.
Make certain Overprint Preview is not active -- View > Overprint Preview - Or the checkbox on the Separations Preview Panel.
Overprint preview tends to do really odd things if it's on and you try to "Save for Web" such as ignoring the visibility state layers, ignoring blending modes, etc..