Set MsBuild Verbosity to find out which assemblies conflict:

http://msdn.microsoft.com/en-us/library/ms164311.aspx

msbuild.exe .\Compile.msbuild /verbosity:detailed
...
  There was a conflict between "xxx, Version=1.0.0.0, Culture=neutral,
  PublicKeyToken=xxx" and "xxx, Version=1.0.12152.1, Culture=neutral,
  PublicKeyToken=xxx".
      "xxx, Version=1.0.0.0, Culture=neutral, PublicKeyToken=xxx" was
      chosen because it was primary and "xxx, Version=1.0.12152.1,
      Culture=neutral, PublicKeyToken=0313e76cb5077f22" was not.
      References which depend on "xxx, Version=1.0.0.0, Culture=neutral,
      PublicKeyToken=xxx" [D:\Projects\abc\bin\xxx.dll].
          D:\Projects\abc\bin\xxx.dll
            Project file item includes which caused reference
            "D:\Projects\abc\src\Web.BuildServer\bin\xxx.dll".
              xxx
      References which depend on "xxx, Version=1.0.12152.1, Culture=neutral,
      PublicKeyToken=xxx" [].
          D:\Projects\abc\src\packages\yyy\lib\Net40\yyy.dll
            Project file item includes which caused reference
            "D:\Projects\abc\src\packages\yyy\lib\Net40\yyy.dll".
              yyy
...

What means yyy references a version of yyy other than the one references by the project or another assembly.

Check the Config files

For Web-Applications the Web.config for all other project types the App.config file (even for class libraries). Make sure you don’t have a section pointing to the wrong assembly version.

Fix the error by binding the correct version.

<configuration>
    <runtime>
        <assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
            <dependentAssembly>
                <assemblyIdentity
                  name="System.Web.WebPages"
                  publicKeyToken="31BF3856AD364E35"
                  culture="neutral"/>
                <bindingRedirect
                  oldVersion="0.0.0.0-2.0.0.0"
                  newVersion="1.0.0.0"/>
            </dependentAssembly>
        </assemblyBinding>
    </runtime>
</configuration>

Helpful utilities

https://github.com/mikehadlow/AsmSpy