This also happens to me sometimes, but not usually on a book I've finished yet. Often I feel it when I have worked on it awhile, but am still in the middle of writing.
Truly, I think the best advice I can give is: change something. One of the writer's great assets is his sense of instinct about when something is right or not right, and I have found that if I feel that something is not right, if I feel awkward about it, you know, it's worth my while to find what it is that is causing it, and then make it different.
Once, that meant cutting out half of my characters and scrapping most of my plot. I had not finished writing it yet, but I had written a great amount of words.

It felt wonderful, though, because the discomfort of having the wrong characters and the wrong plot is pretty irksome.
Usually it's not that drastic, however. Once, I had to change the setting aesthetics, another time I had to rework several scenes, another time I just had to change the name of the book, which gave me a different perspective and solved the problem.
But the main thing is finding out what it is about the book that is making you feel awkward about it. Studying about writing techniques and principles could help you pinpoint it, and thinking over the main purpose and premise of the story could as well.
A book is never
truly finished until it is revised and edited to be as good as you can make it.
