I am unsure of how I solved this, but I've had this same issue before. For me, it had to do with how FM sees the "item" you have stored in a container field. If I used the script steps "insert as picture", "insert as object", or "insert as PDF", I would get wildly different results regarding visibilty on a layout.
That was only further complicated by allowing drag and drop behavior to store documents. Additionally, interactive container fields behaved differently when the field itself was stored in a related table, not the table the layout being viewed was using as it's main data source. I believe it was the related record problem that caused the issue in FM12, but am unable to replicate it in FM13.
Thanks but the PDF's are used to just drop the PDF's into the container... the funny thing is the containers use to work find in FileMaker 12 on both desktop and iPad, but now viewing the container on the Ipad it only shows the icon.. (on the desktop they're still fine..) hence I thought I would use the popover windows to see if they would work that way.. and they don't on both desktop or iPad..
I can still click ont he container and click the VIEW option but it's just an extra step I was trying to cut out.
I'm having this same problem but the popover object is not involved. It happens with a regular container field with a regular layout. No popover at all. You can read about it here:
BTW, the thread eventually wandered off in a different direction and I never got the problem solved. I suspect it is a bug.