How about using "Track Changes?"  You could have each student make their changes with Track Changes turned on and submit it without running "Accept Changes."  That way the submitted document will have a clearly defined list of changes the student has made.  I'm not sure if the Word object model would allow you to extract that list in code but if it did you could have a program read all the documents and spit out the changelist for each student or even only the ones that aren't right.