You must use different accounts to file different tax returns.
If you did use different accounts, then you can try clearing your browser cache and cookies to stop from being automatically logged into the wrong account.
If you tried to use one account, then it is likely that (a) the second return was never filed, and (b) adding the information from the second return actually erased the information from the first return.
Have both spouses received their expected refunds? You and your spouse may want to obtain your IRS transcripts to see what (if anything) is on file for both of you. (You will need separate accounts with the IRS to access your separately filed returns.)
Each tax return for the Online version, requires a separate account with a separate username and password, but you can use the same email address for all of them. If you used the same account for both of your returns, than the second return has overwritten the first return, which means you won't be able to retrieve your return later.