My 3 week old sheltie pup has scab like bumps on her body .You cant see the scabs just feel them,What is this?

She started with a bump on the back of her knee and now they are on several spots on her,You cant see scabs but you can feel the bump.Her front legs do have a little red spot that looked like a scab.She is the runt of the litter.Only one other pup has a bumpy spot on him but just one.What could this be?What should I do?I took them to the vet at 3days old and the spots ont he leg he didnt seem to concerned.Could thes be scabies or flea bites and what signs and treatment is used to cure it?