Is there a way for us to change this?
I outline my novel and in each scene I’ll have some text/notes/etc., which gets deleted as I write that scene. Thus, my writing history for each day is all messed up as it takes the words I wrote and minus it from anything I deleted.
A computer has no way of knowing that the words you deleted are notes. If I write a word, delete it, write a different word, delete that word, and finally write yet another word, Scrivener can only logically count 1 word written, even though I typed out several before deleting them.
To keep your notes separate from the main text of your documents so that you don’t have to delete them (and thus signal to Scrivener that you edited out some words and wrote others), I’d start out with those notes in the synopsis, document notes, or in entirely separate documents.
For the “separate documents” method, you can optionally link to them in the document bookmarks so that they appear in the inspector while still being editable in the main Scrivener editor. This lets you take advantage of other metadata for your notes, snapshots, Scrivenings mode, etc…
Ah, okay, Thanks for the suggestions. I’ll keep them in the notes or synopsis section from now on as those don’t get counted. Kind of a bummer since I already outlined my entire novel. oh well, I’ll use the writing history on the next one.
I ran into the same thing recently, so I feel your pain. If you move all of your notes during one session, then all your future writing sessions will be good at least. 
haha, that’s exactly what I just did! Thanks again for the tips. Happy Writing