What was her issue or beef with Princess Diana that she couldn't let go off and get past? At least momentarily? From what I can make out from the video everybody else bowed? Certainly all of the Royal women in view did. The Queen, Princess Alexandra and Princess Anne. There's no way in my view that the Queen didn't tell members of the Royal family before hand this was her plan hence why they were all in sync especially the Royal ladies. Apart from anything else I think if she hadn't of told them the risk was of some members of the Royal family especially Princess Margaret having a look of absolute horrified shock on their faces at the unexpected surprise of it! That would not have been a good look Infact given the febrile atmosphere at the time it would potentially have been dangerous.
So it wouldn't have been because Margaret didn't know as to why she didn't briefly bow.
I recall reading about ten years ago a former journalist recollecting a story were they were watching the funeral live from their newsroom and as the coffin passed the Palace they whispered to their fellow journalists. 'Look at Princess Margaret. Watch Margaret. See how she reacts to this She still loathes her " Or something along those lines and without fail Margaret delivered by obviously snubbing a royal bow and sparking colourful conversations of royal gossip in the news room about what Princess Margaret thought of Diana.