One of the best ways to avoid problems is to accept all previous changes in a document before it is uploaded to CtrlPrint. (You should also create an IDML of the document, more information about this can be found here.)
Even if you cannot see any markings indicating tracked changes in a document, this does not mean that they are not present. By default InCopy and InDesign track your changes even if they are not visible.
1. Open the "CtrlChanges" palette
From the "Window" menu select "CtrlChanges" to open the "CtrlChanges" palette.
2. Select "Accept All Changes In Document" from the palette
From the additional options menu found in the top right corner of the "CtrlChanges" palate select "Accept All Changes In Document". If the option to accept all changes is greyed out there are no changes in the document.
You should now create an IDML of the document. Information about how to do this can be found here.