You are correct, she cannot file as single since you are still married. You will both need to include each others SSN's on your returns as the spouse.
If she has already submitted her return and is waiting for it to be accepted by the IRS, there is nothing she can do until it is either accepted or rejected. If it is rejected, then she just needs to change her status.
If it is accepted, she will need to Amend her return to make the changes. Amendments are not available until February sometime. This could cause an issue with your return being rejected when you go to file as her SSN would be used as single and not able to be linked to your return, so you may end up needing to print and mail your return.
If she did not submit it, then she just needs to go into the Personal Info section and change her marital status to Married and then say she wants to file separately. To do this she will just click Personal Info>>then the pencil next to her name.
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