It is pretty much unknown. For the police it was a quite hectic time, chasing the Joker and now they had to chase Two-Face. When asked, Nolan responsed with 'I will answer this question one day, but not today'. Shortly spoken, he doesn't want us to know (yet!). Perhaps it will be a subject for Batman 3?
What also could be an explaination is that either Gordon or Nolan made a mistake. Could be either Nolan who didn't count right, or Nolan who made Gordon make a mistake. After all, they're both human
Like much of the film, this aspect has been left ambiguous and up to interpretation. Nolan stated that he may "answer" this question in the future in possibly an interview or possibly a third Batman film, this suggests strongly that it wasn't a mistake on Nolan's part.
iMDB actually has a good summary of the possibilities here, I highly suggest you check it out: