I have already filed jointly on my wife's account for the first time but I am getting notifications from TurboTax about penalties. Is this something I can ignore or is there something I need to do?
If you have an old account of your own but did not use it for your most recent return because you filed a joint return using your spouse's account -- IGNORE the emails. They are just coming from an old account. Keep a record of how to access your own old account in case you need to get to an old tax return--they are saved for seven years. But you only file ONE tax return--and apparently you have done that by filing jointly with your spouse.
The department that sends the emails is not allowed to know whether or not you filed a tax return with a different account or with your spouse. Sounds weird, but it's part of taxpayer privacy. If you filed a joint return with your spouse, you should use that account going forward. You can unsubscribe to emails related to your old account, if you like. You may also want to download and save archival copies of the last 3 years worth of single tax returns (download the pdf of "all forms and worksheets" and save it in a safe place.)