Thanks again, Björn
A finer vertical discretization helped indeed. The accuracy of the solution was not seriously affected, it just showed one "hanging" water body of small dimensions above the main phreatic level, which I was able to identify plotting the water table in 3D view (zero isosurface).
In addition, I've used another strategy to run the simulation using the Free approach: I set Discrete features (Hagen-Poiseuille) in the same join edges as the original Multilayer Wells then I set the the node in the bottom of each well as a Hydraulic head B.C. (instead of a flux B.C., which I believe is the approach used in Multilayer Wells) with minimum flow constraint equal to the time series of pumping in each well (through time series ID) and maximum flow constraint equal to 0 m3/s. In this way, the wells will stop pumping when the water level goes down below the bottom the perforation length.