Hello mathieu,
I am still having troubles with the visualization, saddly i can not share the data. now that being said, in my openfoam simulation I am using a baffle inside the mesh (this are internal faces that are repeated to give different boundary conditions from each side) it is used to simulate thin walls that are simulated as they have a thickness of 0. when i do the CleantoGrid filter (shouldnt it be CleanToGrid ? 
) and I use the opacity different to 1 i get strange artifacts over this baffle zone as one can see in the following image:
I tested the different fitlers you mentioned (clean, cleantoGrid and also clean cells to grid non of them solved the visual issue, any clues?