Why Do We Pay More Taxes Jointly?

You say you take the standard deduction. In that case, you're doing something wrong when you get a better result filing separately. Are you sure you entered "married filing separately" rather than single? The MFS would be for BOTH of you, not just one.

Edit: When both spouses make a substantial income, the withholding tables don't work real well, so it's easy to understand why you end up owing. It's not one or the other person's income that takes you into a higher bracket, it's the combination, and each job doesn't know about the other when the tables are applied so you have to allow for that yourself.

But if you're coming out better calculating as separate rather than joint, you're doing something wrong. This can in rare situations happen if you itemize, but not with a standard deduction.

The reason entering each individually as a joint return looks like a much larger refund is that when you enter only one of your incomes as a joint return, that gets both exemptions and std deductions applied to it, so there's nothing left for the second one when you enter it with the first.

When you "prepare the taxes" with your W-2 only and with her W-2 only, are you still entering your status as MFJ? Then you're taking your deductions and exemptions twice, which of course would seem to give you a bigger refund.

You get those deductions and exemptions as a FAMILY, not as individuals. You take them off your TOTAL income.

File one return, for both of you, as married filing jointly. If it turns out that you owe taxes, then adjust your W-4 forms at work so you're having more withheld next year.

Your analysis is not impossible but is unlikely. It sounds like you are probably making some type of mistake.

Do you have anything besides just a job each? Are you claiming student loan interest, education credits, IRA contributions, etc?

If you really have no credits or adjustments to income you are trying to claim, then your turbotax trials, really do not make sense.