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Is there anything I can do to stop this from happening. Root cause seems to be when the end user is selecting an layer item, then clicks into the open space to deselect, and keeps the map open. If the user uses the Clear Selection Tool to deselect it doesn't occur.
Usually one gets that message if the layer does not have a primary Key assigned in the database such as SQL Server or Oracle. If your data is coming from SDF, there might be a problem with one of the fields...