Maybe it is breed specific, and I have raised no Basenji litters, so I will bow to your greater experience, but I have certainly observed bitches of other breeds disciplining their offspring if they get too rough. Litter mates may yelp, but if they are dominant they may also growl and put the offender in their place, particularly with older pups. From observation I would say that yelping on its own implies submission. My experience has been mostly with pups older than 8 weeks.....and pups from larger breeds. Very young pups seem to have more "immunity", certainly from adults, but as they get older the adults become less tolerant and more inclined to put the pup in its place when things get out of hand. (horses are similar, many foals have teethmarks in their rumps put there by their own dams.....usually geldings are more tolerant than mares!)
With my own 7 year old bitch, she was tolerant of 7 week old Tamu when she arrived and mostly avoided her for the first week, but once she began to play with her, she would snarl and pin the pup down if play got too rough. I never heard her yelp at any time.