I was correcting a document in Word with Grammerly for my boss. I used TRACKING so she could accept changes as she saw fit.
She told me to accept all the changes in tracking. I didn't see how to do that so I just turned it off.
I then continued to correct and when I reached the end of the document, Grammerly said- all correct.
I sent her the document and she said it's filled with errors- so if she wrote"theyre" and Grammerly corrected it to "they're", it's showing in black- no red markings as they are turned off- as
'theyrethey're".
Also punctuation errors are showing as
"." ( she put the period in front of the sentences last quote mark and the correction was to put it behind the quotation mark.

What happened with the document? Why do the words appear like that (the corrections)? Why weren't they just accepted as corrections?

What happened? happened.

This has little or nothing to do with Grammarly and much to do with your Word skills.

There may be more to it in Grammarly, and if so, you need to ask on the Grammarly site.
In Word, on the Reviewing tab there is an Accept button that drops down and lets you select to Accept All.
Track Changes
And, yes, you were right to turn Track Changes off.