The Double Bind by Chris Bohjalian (a pretty good book with a shocking ending but fairly descriptive depictions of a sexual assault including very harsh language).
A key part of the plot of The Double Bind is that the main character was attacked while riding her bike on a long road in a forest. She comes across a photograph of a girl on a bike on this road. The photograph has to be of her. But the picture on the cover is a girl dressed like a business woman, riding a bike through the city, which is possible except that after the attack she gave up bike riding. It's a great cover, it just doesn't flow with the plot of the book.
The Chosen One by Carol Lynch
This book is about a girl in a polygamist cult who complains several times throughout the book about how tightly her braid is braided. She also makes a trip into town two different times and comments about how she would never wear clothing that showed off her body/skin like the girls she sees in town. So while this is an intriguing book cover that made me want to read the book, it doesn't fit with the plot of the book unless I'm supposed to figure that this is a picture representation of how she feels on the inside, or something.