Don't feel alone. If medically appropriate, physicians do tend to err on giving more shots than fewer or none at all. The scenario you describe has happened before to others. Sometimes immunizations have been given to patients who reportedly don't have any list of their previous immunizations. Then their "shot record" is later found and the immunizations that have already been given turn out to be "extra".
Although your daughter now needs to get yet another shot to enter pre-k, I would still be sure she gets it. It's always important to be adequately protected. The benefits do tend to outweigh the risks.