There are a couple of possibilities: the bumps you see are most likely retained hair fragments. These typically fall out on their own following surgery but will occasionally get stuck as new hairs try to grow through. With a clean pair of tweezers, you can remove these non-growing hair fragments (if they are ready to come out, they will slide right out). You can also try scrubbing your scalp with soap and a wash cloth to try and dislodge any non-growing hair fragments. These retained hair fragments are no cause for concern and actually indicate that new hairs are trying to grow.
However, there are also a couple of other possibilities: you might have an infectious form of folliculitis (though this is unlikely since you have seen an improvement). However, if you suspect this could be a possibility, it's a good idea to consult with your hair transplant physician or another doctor. It's also possible that you could have cysts which can be formed if hair follicles are damaged or pushed too deeply into the skin.