Thank you for your reply. I chose for the iso surface the constant to be the interface overlap fraction. 

In the first images you can see how it looks in the stationary and in the last images you can see the rotating cell zone. It seems that the cells in the interface are distorted (I cannot explain by what). One initial guess would be the fact that I have interface in the top and bottom of the cylinder instead of having an interface only in the body of the cylinder, would that be valid? 

Stationary domain : 



For the rotating domain: