I followed the advice of several of the responses here to figure out what was wrong, but none of the answers seemed to explain how to fix it. My issue was that one reference required a different version of a second reference. So Newtonsoft was at version 6, but some other DLL wanted 4.5. Then I upgraded Newtonsoft as one of the other answers suggested and that made things worse.
So I actually downgraded my Newtonsoft install and the warning went away (VS 2017):
Right click References in the solution explorer and select Manage NuGet Packages... Under the "Installed" tab, find Newtonsoft (or whatever your conflict is) On the right side, a dropdown appears next to "Version" that you can change to older versions. It wasn't obvious to me that this dropdown could be used to downgrade.