I think it's because when the floor was originally put in, they didn't put enough clear on it.
So they had to come out again and put another coat (after I argued with the owner) I don't think they bothered to even clean the surface before they put down the second coat so there are parts that look "milky" where you can see it's probably just not adhered because of contaminant.
The pigment is fine on the lifted spot, it basically is the original surface with the clear that is in tact and the second coat is lifting.