I'm already in the habit of checking for words and phrases I tend to frequently overuse: "just then"; "at that moment"; any characters with "blonde" hair. (One time, a beta reader pointed out that every single minor character in my story was a blonde.) But I plan to use the tool to find stealth offenders--words or phrases I repeat without being aware of it.
For example, I just ran the tool against a few recent chapters, and discovered that the word "eyebrows" is repeated four times in five chapters. Yikes. That's a red flag. It probably means I've overloaded some sections with too many of what I call "dialogue tics and gestures": a raising of eyebrows; furrowing a brow; reaching for a drink and taking a sip.
In the phrase frequency finder, I found six instances of "began to." Ack! Either a character does something or he doesn't do it. There's no "begin to." I'll have to go edit those out. The thing I like in particular about the phrase frequency finder is that you can search for phrases of various lengths.
Give these tools a try, and let me know if you think they're useful. Did you turn up any unexpected instances of repeated words or phrases?