I'm only defining 8 pins, but there are gaps in the numbering, so that the numbers actually used match the pin numbers for the same location on a 14 pin DIP.
That square is from a template file. It is intended to be a 0.1 inch square reference object while editing, then should be deleted. I have not got that far with this part yet. What I think you saw was the labelling for the square on top of the actual "1".