Problem with wave boundary conditions
The wave boundary conditions are introducing a small fraction of air in the water phase. This is illustrated in the attached video:
which shows the 0.99 and 0.9999 alpha contours of the $FOAM_TUTORIALS/multiphase/interFoam/laminar/waveExampleStreamFunction case.
The case was run as is.
If run with interIsoFoam instead of interFoam, isoAdvector collects the small amount of air in the water phase into bubbles that rise to the surface. A work around is to run interIsoFoam with surfCellTol = 1e-2 in fvSolution.solvers."alpha.water.*". But really this seems to be a problem with the wave BC's and not with isoAdvector.
A Paraview state file used to generate the movie is attached here: state2.pvsm