Since this is just a user forum, we don't have any access to your data. So it's hard to tell. But since the IRS generally does not want to award people for filing separate returns, it is likely that you have some errors. TT cannot check one return against the other for errors, it can only look for inconsistencies in each return. When you file separately, the easiest thing to miss might be that you can't take deductions on both returns. For instance, premium tax credits, deductions for dependents, earned income tax credits, and so forth.
In general, I would say that if you feel uncomfortable with your married filing jointly return, it might be time to consult with a tax professional who can look at all your actual facts 🙂