Having imported a RTF file into Scrivener, I noticed letters and signs have been added here and there. For instance, “Une fois sorti” becomes “Une fois sSorti”. (The RTF was created from a MSWord 2003 document written in French in case it matters.) It looks like Scrivener incorporates some edits that were made in earlier versions of the Word file (they don’t appear in the final version but I can see them using Markups). Is that a known problem?
Scrivener doesn’t support Word’s Track Changes, so importing a document using this will end up as you’ve described, where all the text is flattened and visible. You’ll need to go through and accept or reject the changes and save that before importing into Scrivener to get a clean version.