As it probably requires to be connected to Subversion repository, here are steps from beginning:

1. Create new project in Unity
2. "Register" in Subversion, using e.g. "svn co file:///Users/johnny/svn/temp_repos_createfolderbug ." from command line
3. Add a material in root of Assets and commit it
4. Create a new folder (without adding it to version control)
5. Drag material into the new folder

Result: Error message "Version Control General: Project is not a subversion working copy." and version control becomes disabled