Sam,
We have had the issue in the past not as much now that I recall. Most times we find it’s a retired benign record (same From/To date) that has been left off centerline because of cartographic realignment. A few things, we use wmx to create our mxds, the point being is we have all the layers in the TOC unselectable at launch minus centerline. This is the first line to preventing the issue. Second, we use data reviewer that has a 1’ buffer around only the locked routes for that user in that version to cutdown on processing time. We use a geometry on geometry check, milepoint over centerline to find any issues before posting. If possible I will have them delete the version and try again as that is better then trying to fix the issue (this goes for most errors) once posted.
As for a fix, on a lower stage I would try reshaping milepoint using trace on centerline to get them back in synch with each other.
Hope that helps. Let us know if that works.