The original is controlled, correct? So - if it changes (officially) it will be replaced. As is noted above, the question is "What is marked?" If the operator, for example, makes notes on the document which do not change the document (such as dimensions) I see no problem. The auditor is going to be suspicious, however, and ask questions: "Why does the operator need to mark up drawings with....?" "If it's important enough for the operator to mark up the document, should those markups not be officially added?"
If you can provide a decent answer, you should be OK. I see this quite a bit in machine shops where operators make notes on prints quite often. The print is controlled, however, so the print (or other document) had best be the latest release.
Barb said: "...someone needs to authorize the mark ups..." which is true if any criteria is changed. I might also discuss the 'markups' with the operator to see just why s/he puts the markups there and whether communication is maintained. If the operator indicates s/he 'needs' the markups, I would have questions about the adequacy of the document in and of its self.
A last thought is consideration as to whether operators take info from one controlled document and put it on another - which I see quite often. In that case there is a problem. If the derivitive document (from where the info came from) changes there is no guarantee that the note(s) on the receiving document will be changed - which is obviously a problem.
Just some thoughts.