We know the divine realm and even the individual’s higher self often decline to remove all karma even when asked, allowing some to remain for growth and learning. Was this the case with Milarepa?

There was a consultation with higher self and Creator to plan and coordinate the sequence of healing events that occurred as a consequence of his service he did in the name of reparations. So he was not astute enough to understand the inner workings, that was taken care of by the higher self in consultation with other beings in the divine realm, especially Creator.