In my humble opinion, ALL molar, and most premolar (with the exception perhaps of single rooted cases) root canals should be done by a root canal specialist whi uses an endodontic microscope. they have more training, and this piece of equipment makes treatment very very accurate.
Is this common for roots to be inaccessible or "missed" altogether? I had a similar situation last year, where a root that they had "missed" got infected. The hardest part for me was the financial burden - they destroyed the crown and post, so I had to pay for new ones -- even though the problem was the doctor's own creation. If he had sent me to an endodontist, this wouldn't have happened.
I am concerned that it has happened again (this year I have better insurance, so hopefully it won't be so prohibitive), because the DDS refused to refer me to the endodontist for a 2nd root canal that I needed, and instead did it himself.
The pain is from the residual infection that is present at a apices of the roots.Sometimes when the dentist does a retreatment the bacteria that is present are activated and cause the type of reaction that you are experiencing. Further treatment with the dentist and the antibiotics are necessary.
IS this an endodontist? If not, you should see one. It sounds like the old filling material was removed and the new filling material has not yet been placed. This means the procedure is not yet done and more than likely infection has set in. perhaps the tooth should be left open for a few days while you are on antibiotics so the tooth can drain.