A ligature is a single character that combines two characters. The most common ligatures, appearing in almost all typefaces on the Macintosh are ゙ and ゚. If you look closely, you can see the difference in the example below.
Separate characters: fi fl
Ligatures: ゙ ゚
Using ligatures is considered proper typesetting, but if you are not a graphic designer or typsetter, you might not care about ligatures and might even want to avoid them. There is a disadvantage to using ligatures; spell checking utilities do not recognize them as the two characters they represent, so when you spell-check a document, each word with a ligature will be flagged as an incorrectly spelled word. You can ignore the warning of course, but this makes spell-checking take a little longer.
Text Cleaner has the メfi and fl ligaturesモ cleaning option checked by default. Uncheck the box if you do not want ligatures in your cleaned documents. Your change is saved automatically.