Error: Orthogonalise a grid which has been clipped by Polygon - Forum - Delft3D Flexible Mesh

Dear all,
I have a large grid for flood modelling of a large area including a city. To reduce the number of cells, I delete some cells inside the buildings with a certain distance from the surface so that the buildings are basically represented by a ring of cells at the surface to allow for momentum exchange (see 0117_Visualization for an example, the polygon line represents the surface of the buildings). The cells inside the houses were deleted using polygons (load polygons --> select delete polygons --> apply to all loaded polygons).
When I now try to orthogonalise the grid, it gives me a couple of error messages, which I am trying to figure out:
* orthonet_assign_xieta: inappropriate fictious boundary cell
* orthonet_comp_ops: orthonet_assignxieta gave error
* orthonet: orthonet_compweights_smooth gave error
I looked into possible reasons particularly for the first error message (so if there is any boundary cell that looks sketchy), but I could not find any. Instead, I observed the following: i created a polygon around an area at stake and tried to orthogonalize the grid inside. It gave above error message.
However, when I subdivided the area using multiple polygons (I used three, and I made sure, that the new polygons always overlap, see 0117_Polygons. The selected polygon represents the large polygon). These smaller polygons combined cover the entire area of the large polygon (and even a bit more). When orthogonalizing inside the small polygons, I don't get above error messages.
Now I am wondering, what the reason for this could be. Is it a bug or did I miss something?
Any thoughts or comments are welcome!
Best Regards, Julius

(P.S. to the developers: It might be super helpful to always show a yellow dot in case of an error in RGFGRID. This is already implemented for folded grid (which I was so glad about, but it would be super handy here as well I think.)