The biggest problem is that gamification tends to provide incentives to improve your efficiency in affecting the "game" portion, to the detriment of the actual thing being scored. As the game becomes more popular, the game becomes what is important.
that's a flaw in the design of a particular the game and not a flaw of gamification itself. What if you could only be rewarded by doing things properly? By trying to affect the outcome of the game you will be improving how you do things normally.