The most likely explanation for this is that you are viewing the PDF in an app that does not support PDF annotations. Many iPhone and iPad apps, including Mail and Safari, do not support PDF annotations. Apps that support PDF annotations include Xodo, Acrobat Reader, and Preview on OS X.

If you want to ensure that your annotations are viewable on iPhone and iPad, you can save a flattened copy of the document. 

1. Tap on the Document Overflow icon on the Action Bar. If you don't see the Action Bar, tap the center of your screen to bring it up.

2. Tap Save a Copy, then tap Flattened Copy from the sub-menu. The flattened copy's annotations are no longer editable but can be seen in any PDF viewer.