Uncharted is a good example of how stages work: https://psnprofiles.com/series/1-uncharted
They're just groups of each game, multiple stacks of the same game will go into the same stage. To get a basic series completion you'd just need to complete one game in each stage.
The concept of numbering the stages is open to change.
You are lying.
You used CFW to edit your SAW trophies. On Oct 6, you accidentally set one of the dates to Oct 9, 2019 12:24:30 PM (UTC). You later saw (heh) this mistake and edited it again to what it is now, Oct 6 12:24:30 (UTC).
So you earned all these trophies yourself, on your own PS4, by playing the game? No one else, or anything could be responsible for the trophies on your account?