I was updating a simple Visual Studio extension that I had written that I also wanted to included in Visual Studio 2012 (it was currently just working in 2013). When I added version 11 (2012) to the supported list I received the following error message upon installation of the VSIX:
This extension cannot be installed because the following references are missing: Visual Studio MPF 12.0
The quick solution for me was to remove this reference (which is listed under the "Assets" tab in the VSIX manifest editor in Visual Studio). I was not using anything I could see from this reference so it made sense (at least to me) remove it. This was an artifact that Visual Studio put into my project when I created the solution originally in VS2013. My first pass just targeted Visual Studio 2013 and worked, it probably has something to do with that not being available to 2012 when I added that onto the supported list after the fact.
Side note, you can also manually remove it from the "vsixmanifest" file by removing the key from the "<Assets>" node in the "<PackageManifest>".