Some lasts have "bottom plates" intended to turn or "clinch" the points of tacks and nails during constriction. Those points are invariably subsurface to the grain of the insole. Clinching the nails "permanently" affixes them.
But shoemakers use nails to attach the insole to the last, as well. These nails must go into the last, they cannot turn on a bottom plate. So half-inch-sized holes are made in the bottom plate to allow the insole to be mounted.
The lump in the middle of the heel is generally where the hole for mounting the insole is. The insole has been driven into that hole and taken an impression of it. It will generally settle.
Smaller lumps are more likely to be paste residues--either the paste (which is often starch or flour based) wasn't mixed thoroughly or moving the heel pad around caused it to bunch up. I seriously doubt that they are heads, or clinched points, of nails although nail are very likely used.