PDF markups created using Acrobat or third-party PDF applications may not appear when placing the PDF into an InDesign file.
This is exceptionally frustrating when the markup is very minor and easily overlooked.
Markups (e.g., added text, lines & shapes, and comments) are not modifications of the original file. They are created separately.
Here are some examples of this issue in a real-world workflow and how to handle it:
In this fictitious illustration of mixed-use development, a colleague provides a site logistics plan. During a review of the draft, it was determined that a construction lay-down yard should be depicted.
You could simply flatten the PDF within Adobe Acrobat but you would loose the ability to edit those portions of the document or you would have to manage multiple versions of the file.
Educating your colleague is the best approach. This lets them maintain ownership of the source and manage edits, while providing you with a flattened publish file.
Remember that in the long run, getting quality files from your colleagues and partners is far better than choosing the quick fix.