I have checked the application, and it works quite well without errors. I have been able to install it on Windows and Mac, and everything worked normally. I checked the No Stopwords option, then pointed the software to the file with the stop words.
The format of the file needs to be TXT or CSV. The software is working exclusively with CSV and TXT files.
However, based on its Help, the words need to be on one line each and in UTF-8 encoding:
"You can select your own file of stopwords provided it has one word per line and is saved in UTF-8 encoding." - Help Section of JFreq.