I am randomly getting gray, unfilled boxes in compiled output. Example below. I’ve searched for anything (notes, tables, etc.) that could be causing this, but the text looks fine. I have experimented with compiling in different formats and the mystery boxes remain, although the text moves relative to them.
Any ideas on what might be causing this?
It does look a bit like a table cell to me. If you enable invisible characters in the editor, you should be able to see table cells that have no borders or backgrounds and are otherwise invisible.
Otherwise, what does the element look like in your word processor—does it let you interact with it, and if so, what types of controls is it giving you?
Update: box shows up in pdf and rtfd compiles, but NOT in docx or ePub 2. If I turn on editing in Acrobat I can select the segments of the box. Can’t select anything in TextEdit. I cannot see any extra invisible characters in or around that part of the text.
If it’s only happening in this one place, it might be easier to just select the text, and a little bit around it as well, cut it and then use Edit ▸ Paste and Match Style to strip out all formatting. Then redo the font and colours as you have them.
I have tried that without success. It has happened several times in this long manuscript. And the text associated with the box moves depending on how I compile (different text ends up overprinted with the box), so it seems to be tied to the page rather than the text. Probably some truly invisible characters ported over from Word (which I abandoned early in this project after discovering Scrivener). Very puzzling.
If you could send us a sample, just a short snippet that demonstrates the problem that would be helpful. I’ve personally never seen anything like that, so all I know is what I see in your screenshot, which isn’t much. 
