The error message reads:
The type 'Microsoft.Phone.Controls.LongListSelector' exists in both '...\Microsoft SDKs\Windows Phone\v8.0\Libraries\Microsoft.Phone.Controls.Toolkit.dll' and '...\Reference Assemblies\Microsoft\Framework\WindowsPhone\v8.0\Microsoft.Phone.dll'
I am using the latest version of the toolkit (Oct '12) and it's a Windows Phone 8 project.
I'm not sure why this is happening and so I don't know what additional information might be relevant but if you have any questions just ask.
I still don't know why it happened but uninstalling the toolkit through NuGet and installing it again seems to have fixed the problem.