Completion/Total Progress

I'm on my 2nd play through, and I've noticed this a few times, but sometimes it's right.

In the progress section, it says I've done 41% of the story, but in total I've only completed 37% of the game, and when i save it, it says (37.2%).

Usually, for me, they either match up, or the total completion is a little more, not the other way around.