Thanks for the additional information. This could be a few things. It could be puppy strangles or swelling of the lymph nodes which comes with infection. It does sound like your pups may have or be developing upper respiratory infections since you are seeing some eye discharge. Infection does cause swelling of the lymph nodes which are generally felt under the ears.. In many cases this develops as a result of the whelping area being too cold.
Pups under 3 weeks of age are not able to control their own body temperature. Thus they can become chilled quite easily which in turn can lead to upper respiratory illnesses including pneumonia. The first week the whelping area should be 90-95F. The second week the area should be 85 to 90F and the third week 80-85F before allowing the room to be a normal temperature. Heating pads can work but the air is still cold and heating pads can get too warm as well and if they move off the pad, they become chilled. Having one room that can be kept warm is much better.
At this point, the room should be warmed to the desired temperature and the heating pad offered as well so if they do become cool they will move onto the pad. Unfortunately, beside making sure they are warm and not exposed to drafts. Clean the pus off the pup with an eye discharge and try to limit that pups exposure to the other though it is likely they will all develop a discharge since they have been together. Keep the discharge cleaned off as much as possible. We use a warm damp wash cloth or warm damp cotton balls. Each pup should have their own so the infection is not passed from one to the other.
It is likely they will need antibiotics so I would plan on having them seen by your vet so antibiotics can be prescribed. Generally you take mom and all the pups in to the office and the vet checks them over. Usually it is done first thing in the morning to minimize the pups exposure to other sick animals so if you can call early that can help get them in quicker tomorrow. Of course if any stop eating or develop other symptoms or seem to be fading, you will need to have them seen earlier.
Now pups who contract herpes also can show signs of an upper respiratory illness. They usually do not nurse well, have painful abdomens and cry a lot. Read more on this here:
It is possible that your pup may have an abscess or "puppy strangles". Puppy strangles is normally seen in pups from 3 weeks old and up. This will require a vet visit. If strangles, your vet will likely treat with Prednizone. You can read more about this here.
However, it could be an abscess from a puncture wound, which possibly occurred at birth. The outer wound heals but bacteria causes swelling beneath the skin. In this case your vet should drain it and prescribe antibiotics. The odds of multiple pups developing an abscess in the same area wouldn't be that likely but I did want to mention it.
Hopefully your female is fully vaccinated because distemper can also first show up as an upper respiratory illness. Most pups get some immunity passed to them from their mothers until they are old enough to be vaccinated.
In any case, they do need to be seen by your vet to determine if this is an upper respiratory infection, herpes or another issue.
I hope this information is helpful to you. If you would like any additional information or have more questions please don’t hesitate to press the reply to expert or continue conversation button so I can address any issues you still have . If you do find this helpful, please take this opportunity to rate my answer positively so I am compensated for my time.