Who was the 1099-MISC made out to: her with her Social Security number or to the S Corp with its EIN?
She probably should have filled out a W-9 for the "other corp" showing what entity was providing the services (this is how the "other corp" knows what name and tax id number to use on the 1099-MISC).
If her name and SSN are on the 1099-MISC, then the IRS will expect her to file a Schedule C on her 1040. If the S corp's name and EIN are on the 1099-MISC, then the IRS will expect this income to appear on the 1120S return.
If you decide to report the income differently from what is printed on the 1099-MISC, be prepared to explain to the IRS why you did what you did, in case the IRS writes you a letter. The IRS will be especially interested if the way you report it happens to save you a lot of tax money.
Note that this issue is subject to some debate. Please look at this discussion at TurboTax's AnswerXchange in which two "superusers" (i.e., very experienced tax professionals) discuss this issue. Reporting the income as actually reported on the 1099-MISC leads to the least number of complications with the IRS...and in the future, have forms W-9 already filled out to hand to your clients, so they send these forms to the right party.
