This may be a suture reaction (stitch material reaction) and however the sutures are possibly removed now from the top layer of skin (they should be) the underlying sutures holding the muscle and connective tissues together are still there. Surgeons normally close incisions by 3 layers of different suture material.
The other possibilty is if sutures were not used in the outer layer and it was staples, then have all of these been removed? - some can dig into the skin that they can be missed at removal (same for sutures sometimes)
If your puppy is licking at the wound she can break down the healing process even at the 3 week post surgery stage. You must apply a "bite not collar" / buster collar / e-collar to prevent this happening.
I would at the moment - Get her checked out just for peace of mind, get them to examine the wound for infection or possibility of missed sutures / staples , it may well be a normal healing process for your puppy , however you do not want it to worsen and normally 3 week post surgery this is not noticable.
Please let me know how you get on xx Happy CHristmas