Hello Nzara,
After some more discussion and research, it seems that the pedestrian areas in question are mistagged. The pedestrian areas tagged with "highway=pedestrian" + "area=yes" shaped linearly (for example Hauptgasse, Gurzelngasse) should be tagged with "area:highway=pedestrian" instead. The non-linearly shaped pedesrian areas tagged with "highway=pedestrian" + "area=yes" (for example Friedhofplatz, Kronenplatz) should be retagged with "place=square".
Would you be ok with me making a changeset to fix this? 