I had this same problem - some users could pull from git and everything ran fine. Some would pull and get a very similar exception:
Could not load file or assembly '..., Version=..., Culture=neutral, PublicKeyToken=...' or one of its dependencies. The system cannot find the file specified.
In my particular case it was AjaxMin, so the actual error looked like this but the details don't matter:
Could not load file or assembly 'AjaxMin, Version=4.95.4924.12383, Culture=neutral, PublicKeyToken=21ef50ce11b5d80f' or one of its dependencies. The system cannot find the file specified.
It turned out to be a result of the following actions on a Solution:
NuGet Package Restore was turned on for the Solution.
A Project was added, and a Nuget package was installed into it (AjaxMin in this case).
The Project was moved to different folder in the Solution.
The Nuget package was updated to a newer version.
And slowly but surely this bug started showing up for some users.
The reason was the Solution-level packages/respositories.config kept the old Project reference, and now had a new, second entry for the moved Project. In other words it had this before the reorg:
<repository path="..\Old\packages.config" />
And this after the reorg:
<repository path="..\Old\packages.config" />
<repository path="..\New\packages.config" />
So the first line now refers to a Project that, while on disk, is no longer part of my Solution.
With Nuget Package Restore on, both packages.config files were being read, which each pointed to their own list of Nuget packages and package versions. Until a Nuget package was updated to a newer version however, there weren't any conflicts.
Once a Nuget package was updated, however, only active Projects had their repositories listings updated. NuGet Package Restore chose to download just one version of the library - the first one it encountered in repositories.config, which was the older one. The compiler and IDE proceeded as though it chose the newer one. The result was a run-time exception saying the DLL was missing.
The answer obviously is to delete any lines from this file that referenced Projects that aren't in your Solution.