To reproduce the issue on Mac OS X:

1. Open the WD.
2. Open the "RNA-seq analysis with Tuxedo tools" sample.
3. Click the "Setup" button in the opened wizard.
4. Click the "Next" button.
5. Click the "..." button to select "Known transcript file".
6. Select the file browsing mode as shown on the attached screenshot: this mode allows to expand directories without selecting them.
7. Select a file in an expanded, but non-selected subdirectory.

Expected result: the file path must be correct, file is selected with the first "Save" button press.
Actual result: the file path consists of the selected directory path and the file name.

Note that there is no such error in the UGENE open file dialog. Maybe it makes sense to reuse common code.