Wrong version of .NET assembly getting copied to Web Forms bin directory

I'm working on an ASP.NET Web Forms web site and frequently get run-time exceptions like the following:

Could not load file or assembly 'Newtonsoft.Json, Version=4.5.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040)

=== Pre-bind state information ===
LOG: DisplayName = Newtonsoft.Json, Version=4.5.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed
 (Fully-specified)
LOG: Appbase = file:///C:/Code/MyProject/
LOG: Initial PrivatePath = C:\Code\MyProject\bin
Calling assembly : System.Net.Http.Formatting, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35.
===
LOG: This bind starts in default load context.
LOG: Using application configuration file: C:\Code\MyProject\web.config
LOG: Using host configuration file: \\foo\bar\Profile.v2\simonm\Documents\IISExpress\config\aspnet.config
LOG: Using machine configuration file from C:\Windows\Microsoft.NET\Framework\v4.0.30319\config\machine.config.
LOG: Redirect found in application configuration file: 4.5.0.0 redirected to 11.0.0.0.
LOG: Post-policy reference: Newtonsoft.Json, Version=11.0.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed
LOG: Attempting download of new URL file:///C:/Users/simonm/AppData/Local/Temp/Temporary ASP.NET Files/vs/8d6ca9e7/1d38a78a/Newtonsoft.Json.DLL.
LOG: Attempting download of new URL file:///C:/Users/simonm/AppData/Local/Temp/Temporary ASP.NET Files/vs/8d6ca9e7/1d38a78a/Newtonsoft.Json/Newtonsoft.Json.DLL.
LOG: Attempting download of new URL file:///C:/Code/MyProject/bin/Newtonsoft.Json.DLL.
WRN: Comparing the assembly name resulted in the mismatch: Major Version
ERR: Failed to complete setup of assembly (hr = 0x80131040). Probing terminated.

They're invariably because the "wrong" version of an assembly (it always seems to be Newtonsoft.Json) gets copied to the Bin directory despite the fact that the packages.config in the root of the site has:

<package id="Newtonsoft.Json" version="11.0.2" targetFramework="net45" />

and the web.config contains:

<dependentAssembly>
<assemblyIdentity name="Newtonsoft.Json" publicKeyToken="30ad4fe6b2a6aeed" culture="neutral" />
<bindingRedirect oldVersion="0.0.0.0-11.0.0.0" newVersion="11.0.0.0" />
</dependentAssembly>

Can somebody please explain what dictates which assembly gets copied to the Bin directory, why this keeps happening and how to prevent it from happening in the future?

I guess, that some of your used frameworks/libraries are using different versions of Newtonsoft.Json. First, check your frameworks/libraries if they are requiring different versions of the Newtonsoft.Json library.

When you detected which is the (minimum) required version of Newtonsoft.Json try to reinstall this version through Nuget.