Like @JerSchneid, my problem was empty directories, but my deployment process was different from the OP.
I was doing a git-based deploy on Azure (which uses Kudu), and didn't realize that git doesn't include empty directories in the repo. See https://stackoverflow.com/a/115992/1876622
So my local folder structure was:
[Project Root]/Content/jquery-plugins // had files
[Project Root]/Scripts/jquery-plugins // had files
[Project Root]/Scripts/misc-plugins // empty folder
Whereas any clone / pull of my repository on the remote server was not getting said empty directory:
[Project Root]/Content/jquery-plugins // had files
[Project Root]/Scripts/jquery-plugins // had files
The best approach to fixing this is to create a .keep file in the empty directory. See this SO solution: https://stackoverflow.com/a/21422128/1876622
