The odd way WF treats Workfront Proof (PHQ) information has confused us from Day 1. I instruct users not to use the Task/Document quick-look summaries as a source of truth, nor the info in the Updates stream sent from PHQ.
They are instead instructed to use the links that appear when you hover over the proof document (Proof Details, Proof Summary, etc.) or to go into the proof (i.e., open it in PHQ).
The other one that trips users up is while it makes sense to do replies to a comment as sub-items, exports to a PDF do not reflect this (Adobe doesn't support it). For example in PHQ, I can have Comment 3, 3.1, 3.2 but the PDF will count these as three separate comments and renumber them (causing a disconnect between PHQ and Acrobat). Not sure what a good solution would be, but this disconnect is confusing in workflows like ours where a PDF checklist offline is more handy than viewing everything in PHQ.