"Runt of the litter" went from being a livestock term referring to the baby animal that had the least chance of surviving to adulthood because of genuine issues aside from mere size to being a jokey term for the smallest person in the family, etc.
A literal "runt" in dog terms would be something like a puppy who had genuine development problems. The puppy that isn't growing, that isn't reaching the basic developmental milestones (eyes opening, crawling, nursing, standing, walking, etc) with any kind of regular pattern. Maybe it can be coaxed and babied into eventually being okay, but maybe not. Something's actually WRONG with it.
Reaching the milestones a day or two behind other puppies is sometimes just a fluke, and that baby winds up being the biggest of all the pups, perfectly happy and healthy and smart. In fact, most of the time that's the case.
The original poster indicates that her puppy is just as active as the others. If she's eating and pooping and peeing and making mischief, all the while making steady gains in size and weight, you don't have much cause for concern.
If the difference in size becomes more pronounced in the weeks to come, or she doesn't enter some new developmental phase, then it's worth checking out to make sure she's physically fine.