I think you can ignore it now. Later, when you will write out the GDS file, and run DRC (Calibre or Hercules), these violations will disapper. You see them in PnR (ICC) tool, because it works with some kind of abstract view (FRAM for ICC). In this abstract the pins are just a small portion of metal. But, in the real layout of macro block (CEL view or GDS), these pins are bigger, they have long metal wires, connected inside. So, when you run DRC on the complete layout, you will not see min area violations (because, macros provider check their product with DRC tool and fixx any errors before selling them to you). It's a usual case.
Still, some macros may have real min area violations - in this case, it should be mentioned in macros app. notes (or datasheet).