There was nothing particular about those spots themselves, just an arbitrary spot in the lake. I might have fat-fingered the shift key, and reading Morsk say that I placed concrete on top of concrete might have something to do with the super-force-build mechanic.

Trying to replicate it like that ...

And if anyone knows how to manually remove it with debug maybe let me know

I was using the cut tool (with the shortcut crtl+x) to move some walls and concrete a few tiles.

After that I wanted to remove the landfill under it (which I also did with the cut feature) which went well for most of the landfill, but 4 tiles (seemingly random to me) seem to have lost its tile ...