"The Avian Egg" indicates that abnormal yolk shapes are the result of variations in strength of the vitelline membrane that surrounds the yolk. Weaker parts of the membrane allow the yolk to bulge out to form the corners of the square. These formations are very rare and can be heart-shaped, U-shaped, triangular, etc. It is possible that a certain hen always produces yolks in this unusual shape.
This abnormality would not affect the safety of the eggs.