Well, I did some additional research before to open a case with NetApp and my problem seems to be like this: Unexplained LUN trespasses on EMC VNX explained
I have disabled VAAI temporary to make a test, and the problem disappears, so I guess it could be the same thing.
In theory the movement of the LUN out of the preferred controller is done to improve the response, and in a Round Robin configuration the LUN should be restored to the preferred one afterwards ( https://community.emc.com/thread/132762 ) but this seems not to happen.
Anyway I think I have an explanation to this behavior and I will contact NetApp to see if it is like this or there is something else.