Gone Girl ... After I finished the book I just sat here wondering, "Really?" It just didn't make sense to me. Then a friend told me that was one book where you really needed to see the movie before reading the book. So I saw the movie and read the book again. She was right. The second time around it made sense.
The Martian ... I really think the movie flowed better. But then, if I recall correctly, the book was really written more like the character was keeping a journal.
Divergent ... I remember while watching the movie there were things they changed that bothered me. Things that didn't change the outcome but I just didn't understand why they felt like they needed to change them. One thing that did stand out to me is that in the book Tris is described as being very petite and small and in my mind that was part of why she was picked on. But Shailene Woodley, the actress who played her, is 5' 8".
There are others in the list where I read the book and saw the movie, but I really don't have opinions on those.