IF she filed as single or married filing separately, and IF you just filed a joint married return (married filing jointly), then the joint return will automatically cancel the separate or single return. However, if she got a refund from her separate return, that will eventually have to be paid back, since the joint return won't know that a separate return was also filed. You should wait for the IRS to send a bill, or they might adjust the refund claimed on the joint return. Either way, expect to have to pay that back one way or the other.
Alternatively, the other way to fix the fact of her filing separately, is for her to file an amended return that changes from separate to joint, and adds you and all your information. Amended returns can't be e-filed, they must be printed and mailed, and they include an extra form 1040-X. If you did this, you don't need to do anything further.
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It sounds, though, that you may be confused on what you actually did.
If you are using Turbotax Online, each account can only prepare and file one tax return. So if you were logged into her account, then you probably didn't actually file a second return, you only changed the account without sending those changes to the IRS.
Also, be aware that if you electronically submitted a joint return listing your spouse, it probably would have been rejected due to a duplicate SSN (since she already filed). (Maybe it would have been accepted if you were changing from single to joint but I don't think so.)
Start by trying to locate whether you have one online account or more than one account. Use the account recovery tool and check all the email addresses you or she might have used. (You may need to clear your browser cache and cookies in between attempts). https://myturbotax.intuit.com/account-recovery/ Print a copy of each tax return you can find.
Then, use the Turbotax e-file checker to see whether or not you really submitted one return, or two returns. Be aware that with a joint return, you use the SSN of the person listed first. https://turbotax.intuit.com/tax-tools/efile-status-lookup/
Then do the following:
If you confirm that two returns were e-filed and both were accepted, wait for the IRS to take the next step. (But I suspect this did not happen.)
If you confirm that your spouse's return was accepted, but your joint return was accepted, you have two possible options.
a. Mail the joint return.
b. Forget the joint return and prepare an amended return from her original account.
If you find that you changed your spouse's account but never actually filed it, you will have a problem since changing the file without using the amending process will make it impossible to actually file an amended return. I would suggest you start a new account to prepare a fresh joint return and mail it in. (You will be rejected to e-file due to duplicate SSN.) Remember to make plans to repay your wife's tax refund.
