It is extremely rare that MF Separately is to your benefit, so I hope you have been doing them correctly. Are you in a Community Property State? Do you both itemize?
On the other hand, it is common for a married couple who both work (or an individual who has two jobs) to owe taxes, because of increasing Federal tax brackets. Going forward, you can mark your W-4 forms as Married but Withhold at Higher Single Rate and/or elect to have a flat dollar amount withheld for taxes. This may be helpful:
Should You and Your Spouse File Taxes Jointly or Separately? - TurboTax Tax Tips & Videos (intuit.co...
