I believe it is from this line:
addIoFiller -cell EMPTY1LB -prefix if1 -fillAnyGap
Check standard-cell documentation if the EMPTY1LB can be overlapped.
The errors may be false violations. Ignore it if this is the case.
You'll learn in time that the tool is just limited in capability & sometimes engineers can't be bothered to make the tool know every single false violation to waive.