Sometimes when deleting a module under modules/android directory in project with the directory structure containing MY.PACKAGE.ID/VERSION.NO with inside having documentation, example, libs, lib and some more directories and files is deleted in Titanium Studio, the directory structure sometimes remains though all files under it got deleted.
If you copy select some module folder, put this inside modules/android and then delete it. Now open up the folder in your finder (or use the commandline), refresh and the folder will sometimes still be there.
Note:This does not always happen though, can only be reproducible at once every 5 to 10 times. Try it with 5 minute intervals until you can reproduce it.
Also, please find the attached video representing the issue.