Hi Zoltan,
This is an interesting point that you are raising. There are known issues with the geolocalisation of the pixels and the associated uncertainties in the Sentinel-3 images provided by ESA (via Copernicus Open Access Hub), but I haven’t seen any concrete information on how to deal with the issues being published by an official source.
You might find the following blog article interesting: http://blog.imagico.de/sentinel-3-a-first-look-at-the-data-part-2/.
If you want to get down to the bottom of this problem I would suggest you contact ESA or the Scihub support (eosupport@copernicus.esa.int). Please let us know if you find something interesting 
Maxim