This is a Mac OSX feature. Any time a file is set as stationery (a reference copy not meant for students to change) and you open that file, the Mac OS makes a copy of it. All applications do this, not just Logger Pro.

The experiment files we supplied with Logger Pro 3.1 are set as stationery files to keep students from changing them.

Some users do not like this feature of OSX, so in Logger Pro 3.2 and newer, we no longer use the stationery flag to protect the experiment files. We use another method to make it difficult to accidentally overwrite the supplied experiment files.

If you do not like the automatic copies of files, update to Logger Pro 3.2, a free update from 3.0 or 3.1.