Whenever I end a sentence in a text with an ellipsis and space, as in:
“Thank you. Dreadfully sorry, but… “
the editor responds to a following double quote mark by substituting an opening, not a closing double quote. The conversion to smart quotes fails because of the space character. Leave out the space and the quote closes properly. The rules on ellipses allow for including spaces on either end of the three dots, but not requiring them. I suspect this is an editor error and not a Scrivener bug, though I’m hoping that’s not the case as if you don’t have visibility into the editor’s code you cannot fix this.