Yes, charges could be filed if the District Attorney decides to do so. The best short-time advice for the two of you is to refuse to discuss the case with anyone – including the girl, her family, or the police. If the police come to her and act like they want her side of the story and express doubt that the girl is telling the truth, don't be fooled. The police do this often in an effort to get the suspect to open up and trust the police. Also note that if the girl or one of her family members call your wife on the phone, there is a good chance that the call is being made (and recorded) at the request of the police, in hopes that she will say something incriminating. This is a very common technique used to prove these types of cases.
Depending on your resources, your wife may wish to consult with an experienced attorney to guide you through the investigation and suggest certain steps to take in order to put her in the best position in the event charges are ever filed.
Best of luck to you both.
I don't agree with the first answer. I don't think any prosecutor will entertain charges against the girl. They may entertain charges against giving alcohol to a sixteen year old and after that, the best you can do is defend false charges against your wife with witnesses.
Best to get witness statements now while they're still fresh.
Theodore W. Robinson's reply is dead wrong. Not only is it obvious that he didn't read your question carefully, he is not licensed in California.
As Mr. Gurwitz noted, you are concerned about possible charges being filed against your wife, not the girl who is making the allegations. Since the accuser is sixteen years old, if your wife is charged with a crime for fondling her, the most likely offense would be Penal Code 647.6, annoying or molesting a child. Although it is a misdemeanor, there is the potential for jail time; even worse, it calls for lifetime sex offender registration. (If the girl was younger, or the conduct went beyond touching, there is potential for felony charges to be filed.)
Mr. Robinson's advice to start taking witness statements is also ill-advised. As Mr. Gurwitz noted, the best course of action is not to discuss this case with anyone and, if you can afford it, hire an attorney who can advise you and direct the investigation. It is ALWAYS better to have a private investigator conduct witness interviews; if you try to do it yourself, you wouldn't have an independent investigator to impeach a witness who later tells a different story or, worse yet, accuses you of trying to force them to give a false statement. It may also look like you were trying to discuss the case to get your stories straight, and one of the first questions any half-competent prosecutor asks is whether a defense witness talked with the defendant about the case.
Defending yourself against criminal accusations is not a do-it-yourself project like fixing a leaky faucet that you can handle with a little bit of advice from the Internet. It's always best to consult with a criminal defense attorney in your area; most will give a free initial consultation.
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.