Always keep good records of legal matters. Your situation shows how sloppy record keeping can turn a simple problem into a disaster.
Do you have any proof of what you did? Did you mail a check to the court? Do you have a canceled check? If you mailed a check to the court, but it didn't clear your bank, did you follow up to see what happened? Do you have a copy of the citation with the officer's signature, showing the date you got proof of correction?
In my office, important legal documents are sent to the court by courier service or Federal Express. We always include extra copies, along with an envelople addressed to my office that already has stamps on it, and a note asking the clerk to send back "conformed" copies. That way, we have a copy of the documents with the court's stamp, showing they were received and filed. Any court fees should ALWAYS be paid by check, money order, credit card or some other kind of payment method that can be traced later; if you have to pay cash, get a receipt and DON'T LOSE IT.
You can ask the clerk of the court if you can get the case back on calendar for a possible reduction of the fine or bail. Make sure that you take the registration paperwork, showing the car was currently registered at the time. However, if you don't have the kind of proof I've listed above, you may have a very hard time proving the mistake was the court's, not yours.
Please understand that this is a general discussion of legal principles by a California lawyer and does not create an attorney/client relationship. It's impossible to give detailed, accurate advice based on a few sentences on a website (and you shouldn't provide too much specific information about your legal matter on a public forum like this site, anyway). You should always seek advice from an attorney licensed in your jurisdiction who can give you an informed opinion after reviewing all of the relevant information.