I have had quite a bit of experience with Xamarin in the past and the company I work for is now doing cross-platform development including the Mac. Because the Xamarin/Nuget integration doesn't quite do all of the things we need, we have a custom solution to deploy all NuGet package files into a well known folder within the root of each branch. This has worked very well in Windows for some time and it works fairly well in OSX Xamarin Studio - but there is 1 gotcha.
If you do a complete clean, open the solution, download/extract all packages (we have a special .csproj in the solution that does this via MSBuild), and then build, Xamarin Studio doesn't see the assembly files - even though they're in the proper directory. The relative paths are all valid too. To workaround this, all you have to do is close the solution and re-open.
We're not quite sure why things fail but are wondering if Xamarin Studio is caching files as soon as you open the .sln? If so, is there any way to change this behavior? I'm willing to bet you could easily reproduce this by simply opening a solution w/ 1 assembly file references, ensure the folder is empty, open the solution, copy the assembly into that said folder, and then confirming that the build fails.