I wanted to post pauloya's solution they provided in the comments above. I believe it is the best solution for finding the offending references.
The simplest way to find what are the "offending reference(s)" is to set Build output verbosity (Tools, Options, Projects and Solutions, Build and Run, MSBuild project build output verbosity, Detailed) and after building, search the output window for the warning. See the text just above it.
For example, when you search the output panel for "conflict" you may find something like this:
3> There was a conflict between "EntityFramework, Version=5.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" and "EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089".
3> "EntityFramework, Version=5.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" was chosen because it was primary and "EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" was not.
As you can see, there is a conflict between EF versions 5 and 6.