Thank you for your post.
After setting up a FileMaker Pro 14 file with two Interactive Container fields (one local storage, one remote storage), I inserted a PDF file into both Container fields. I then opened the hosted file using FileMaker Go under iOS 9.3, and I was able to access both Container fields. I then updated to iOS 9.3.1, and I was still able to access both Container fields.
I then uploaded the file to FileMaker Server 14, opened the hosted file using FileMaker Go, and I can still access both Container fields and view the PDF files.
Since iOS 9.3.1 doesn't appear to be the issue, try creating a new file in FileMaker Pro 14, create two Container fields with the second one having remote storage. Set the formatting of both fields to Interactive content. Turn on Network Sharing.
Open FileMaker Go, and access the hosted file. Does this work? If so, then upload the hosted file to FileMaker Server, and access the FileMaker Server hosted file. Does this work?