Seems like you may have connectivity issues between the walls with the holes and the ones orthogonal to those. One suggestion would be to mesh the walls with the holes first using polygonal meshing. Subsequently use the Geometry > Generate Slab Wall Connection feature to generate the mesh in the orthogonal walls which would honor the meshing used for the walls with the holes. This feature can be accessed through the top menu and when meshing the orthogonal walls without the holes, all you need to do is select the 2 corner nodes of the wall with hole first and then select the other two corners of the orthogonal wall. The number of divisions to be used for the common edge between the walls is already read from the existing mesh and you just need to specify the divisions along the other edge, when meshing the orthogonal wall.
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