I had this same issue and it was not a code problem.
I was using the publish option (not the FTP one) and Visual Studio was not uploading some of my scripts/css to the azure server because they were not "included in my project".
So, locally it worked just fine, because files were there in my hard drive.
What solved this issue in my case was "Project > Show all files..." and right click the ones that were not included, include them and publish again
