My understanding from talking to a friend at Adobe (but some time ago, so I might be misremembering) who knows more about PDF than anyone on the planet is that PDF truly is a standard, but there are lots of implementations of various versions of the standard, many of which don’t do a good job. Apple’s implementation falls into that category. And interoperating between multiple mediocre implementations can cause headaches.
Adobe Acrobat is probably the closest you can get to a reference implementation. I’m not fond of the app, but it’s the best bet for any tricky PDFs.