The build Output window should give you a fix/workaround for this problem.
Clean and rebuild the solution.
Examine the contents of the Output window, look for this text:
Consider app.config remapping of assembly "AjaxControlToolkit, Culture=neutral, PublicKeyToken=28f01b0e84b6d53e" from Version "4.1.40412.0" [C:\Visual Studio\App\Lib\bin\Debug\AjaxControlToolkit.dll]
Following this there will be a fragment you can paste into the <assemblyBinding> section of your web.config.
C:\Program Files (x86)\MSBuild\14.0\bin\Microsoft.Common.CurrentVersion.targets(1819,5): warning MSB3247:
Found conflicts between different versions of the same dependent assembly.
In Visual Studio, double-click this warning (or select it and press Enter) to fix the conflicts;
otherwise, add the following binding redirects to the "runtime" node in the application configuration file:
<assemblyBinding xmlns="urn:schemas-microsoft-com:asm.v1">
<dependentAssembly>
<assemblyIdentity name="AjaxControlToolkit" culture="neutral" publicKeyToken="28f01b0e84b6d53e" />
<bindingRedirect oldVersion="0.0.0.0-16.1.0.0" newVersion="16.1.0.0" />
</dependentAssembly>
</assemblyBinding>
Once you paste that in and rebuild it should automatically reference the version of the Toolkit specified as the newVersion.
reference the 'AjaxControlToolkit, Version=3.0.20820.16598, Culture=neutral, PublicKeyToken=28f01b0e84b6d53e' assembly to your project or put it in the GAC.