I think it is just a bug in Visual Studio, which has been there for quite a few VS version, at least with VS2010 that I currently still use along with VS2012/2013.
You can select any one of the repeated item as the reference. Then, if you open the References dialog box again, you would see all the repeated same items are flagged as referenced.
Note, when you use AutoCAD COM API, you do not have to go to reference dialog box's COM tab, if you have downloaded ObjectARX SDK. You can browse to ObjectARX SDK folder and set reference to the COM interop assemblies coming with the SDK.
Also note, older AutoCAD (at least up to Acad2012), the COM Interop assemblies are installed into GAC when AutoCAD is installed, So, in your project, the "Copy Local" to the interop assemblies should be set to "False". Since Acad2013 (or 2014? my memory is vague on this, because I rarely use COM API these days), AutoCAD stops installing COM Interop assemblies into GAC. in this case, you need to make sure the COM interop assemblies go with your add-in assemblies together.