It’s actually a styling decision by the developers of that map style. You’ll need to “cut a hole” in the pedestrian area for it to appear. In a sense that’s correct - the pedestrian area doesn’t “extend underneath” the guildhall I guess.
After some thinking: making holes is perfectly sane way. Squares are not necessary the same as pedestrian areas, they can contain buildings, green patches, fountains etc. You should tag square with a place=square (with no holes, of course) to indicate that both pedestrian area and building belong to the same square.
I would do it the opposite way. The relation should be the pedestrian area, because that’s the one that needs the holes cut out of it. Then, the outer way can be the place=square, which would cover everything inside that way (including the holes, because the way doesn’t have anything cut out of it).