It should soften (or break in) with enough wear, I haven't had any heel/Achilles issues with an NMD yet, but a pair of Yeezy 350s did something similar. The area eventually softened up.
PK has a more elastic ankle collar that feels softer from the get-go. Although, some people have complained about the rubber heel counter digging in. Also, normally the branded pull tab has a tendency to mildly rub as well in some cases (since it ends up folding inward from the factory), but it eventually starts to fall the other way after enough use or tugging on it to slip on the shoe. Some people expedite the process by taping it down so that it falls the other direction.