That kind of touches on things in The Matrix which are really hard to show someone else - some of the subtleties - I'd have experiences in life which would suddenly give me an understanding of what the writer was intending or motivated by, etc. at various points such as the background of characters and what motivated them to be the way they are in the movie and once you understand that you see certain events or paths in the movie in a whole another light which then potentially unlocks understanding something else in the movie you never saw the significance of before.
There is a good write up on some of it if I can find it where they played around with what happens if some of the character's motivations are actually different to what we think i.e. The Oracle being truly evil, etc.
It is largely absent in the movies which come after.