What you're experiencing is a limitation in the PDF readers on all mobile devices. Many of them do not support all the interactive features like buttons and video.
Here is an article I wrote a few years ago, but it's still mostly true:
You'll need to buy a PDF reader like PDF Expert (Readdle, $US 9.99) to view some of those features.
Thanks for the response but actually the pdf had been working fine with our ipads for about a month and a half. All the hyperlinks and interactivity didn't have ANY reported problems on the ipads up until about two weeks ago when suddenly huge parts of the document would disappear when clicked or some parts like menu items just don't appear at all. I mostly just wanted to see if anyone else had been experiencing this issue in the past few weeks.
What PDF reader are you using? That's likely where the problem lies.