Updates often fail in Windows
I use Windows 7 Professional at work, and I often find myself with locks on directories, preventing some command line runs to work, particularly when they must remove a file or folder. These locks are made by GUI applications, from Windows Explorer itself to Eclipse or Atom (or SciTE, the editor I use to quickly view any file).
It might be the reason why package updates often fail. Sometime they work, sometime not. Sometime they fail with a relatively explicit message (like "cannot delete some path"), sometime with undefined:

This time, I had the console opened, so I can show the corresponding stack trace:

I don't know if you can do something on the locking issue, but perhaps you can do a better error extraction to show a significant message... For locking, maybe I can have better results by closing Atom, putting apm in the path, and using it to update, but that's not very convenient.
Another issue: once an error has been issued, I cannot retry to update the package.
In my case, working on files/folders via CLI fails when I have the file/folder open in Atom, such as having the folder selected or expanded in the Tree View. When I select another item, like the parent folder, I'm able to do the CLI work on those files/folders again that I wasn't able to.
I'm on Windows 10 myself.