Strangely this issue only affects a single file which we will call test.lic. test.lic is an xml file and is located in the root folder of an asp.net mvc project.
The file properties are:
Build Action = "Content"
Copy To Output Directory = "Never"
Other files in the root folder with the same settings (i.e. robot.txt) are included in the publish output. Changing Copy to Output Directory seems to have no effect