Hi Palary,
would you mind to refer to the CS you restore with a link in the changeset comment tag or the its source tag. This makes it much more transparent.

As I wrote earlier, the `covered=yes` tags are probably ok but the highways should not be connected with the building. It might be true that the buildings are mistagged but to solve the JOSM Validator warning you probably just need to add `layer=1` to the building.

Cheers skyper