As a general rule you should always update your NuGet packages in bulk for a solution. And if you do pull in projects that have different versions of packages, you should make sure that the Assembly redirects in each project are updated to redirect to the latest version in use (especially for JSON.NET which is one of the worst offenders due to its strong name signature on the assembly).
Here's a post that describes how you get your assembly references updated in the entire project:
http://weblog.west-wind.com/posts/2014/Nov/29/Updating-Assembly-Redirects-with-NuGet+++ Rick ---
>Hi everybody,
>
>I've been trying to install latest MVCScaffolding.2015 in my VS 2013. While doing that I noticed that several of packages used in our project have an update, so I decided to go for it and updated a couple (EF, NetJson, etc.). Now I'm getting this error:
>
>Error 3 The type 'Newtonsoft.Json.JsonIgnoreAttribute' exists in both 'c:\Program Files (x86)\Microsoft Visual Studio 12.0\Blend\Newtonsoft.Json.dll' and 'c:\_Siriusware\Main\SysManager\packages\Newtonsoft.Json.7.0.1\lib\net45\Newtonsoft.Json.dll' C:\_Siriusware\Main\SysManager\SysManager.Web\Areas\Guests\Models\EditPrefsGuestsViewModel.cs 224 10 SysManager.Web
>
>What should I do to resolve it?
>
>Thanks a lot in advance.
>
>UPDATE. Looking into this right now
>
>
http://stackoverflow.com/questions/21653130/newtonsoft-json-exists-in-both-blend-newtonsoft-json-dll-and-solution-pa>
>UPDATE 2. Yes, I resolved the problem by removing the other references in the project file.