About two years ago I had to have a filling in one of my back teeth fixed because decay had spread. The dentist told me it might fix it but I would probably have to have a root canal someday. This fixed it for a while but shortly I began having pain when I chewed on that side. However it didn't bother me much so I left it. Two months ago I started a new job and I decided to have the tooth fixed once I started receiving dental benefits. However 6 weeks into the new job I started having severe pain in the tooth. I went to the dentist and they said I had an abscess and perscribed penicillin to clear up the pain in the meantime. The meds took away most of the pain but they told me I could do a pulpectomy for now and once my benefits kicked in I could get a root canal. So I opted for the pulpectomy. I had it 3 days ago and it is hurting quite a lot. It hurt severely after the freezing came out and then it got better but now it's bad again. The dentist said it might be sore for a day or two but it seems to be hurting more than it should and for that matter if they removed all the pulp in my tooth what is left in there to be causing pain? I feel like this is becoming a dental nightmare.

A pulpectomy is a root canal that is usually done on baby teeth. The procedures are pretty much the same except the material that is used to fill the cleaned out roots may be different. They may not have gotten to the apex (tip) of all the roots or have cleaned out all the nerves for that matter, sometimes there is an auxiliary canal that the dentist isn't aware of.
I'd suggest going back to the dentist if pain medication isn't helping in the next day or two.