As soon as she gives the money back to the Bank, she will have to pay gift tax on it.
No she won't. It isn't income to her and it isn't a "gift" to the bank. It's a mistake. No 1099 should be issued, nothing should be out of whack on her W-2, the IRS should never know about it at all.
If, by some fluke, she were to be audited, she would have records that there was $98k deposited and $98k withdrawn. It's a pretty simple and straight forward explanation....plus it has the advantage of being the truth.