If I use a cliche idea (ex. Prophesy) to explain part of the plot better in a fantasy book, does it lower the value of my story?

I’m going to say “potentially”. Prophesy is good for information but not cause. Something should happen AND it was prophesied to do so. Not something happens BECAUSE it was prophesied. Your question doesn’t necessarily imply that, but I just wanted to put that out there.

Now this is completely subjective, but I find prophesy works best when it’s accuracy is only obvious in hindsight. The best example I’ve seen of this is in ‘The Wheel of Time’ series. In book 1 Robert Jordan uses Min to “prophesy” different things about the main characters. ALL of them come true, and most of them not until many books later. It’s a LOT of fun to finish the series, and then go back and re-read what Min said and map how those things were accurate or came true throughout the series.