Using the autotools project type, when you modify any of the Makefile.am or configure.ac files, and save, the source files are duplicated in the project view each time.  This leads to 2,3,4 etc.. copies of the same file appearing in the list of files.  Closing Qt Creator and reopening the project fixes the issue, but then any modifications cause the same issue to start again.  A workaround is to create a "Non-Qt project" and just add Makefile.am and configure.ac to the files.