I filed jointly with my wife on 5/14/2019. she originally filed for an extension because she is in the military prior to April 15, 2019. We were originally going to file married but separate because we weren't ready to file taxes before April 15th, as a result, she got the extension and I didn't file on the due date. On May 14, 2019 we decided to file jointly under her tax return and submitted it that day. We are due a federal refund but owe state taxes which we paid on May 14, 2019. Will we still receive a penalty for filing late even if we did it under her tax return and she filed an extension? If so, how much if we owed $544 for state taxes? Am i going to be charged the failure to pay penalty plus the failure to file penalty? Since we paid the $544 on May 14, 2019, how do we know how much the penalty/penalties will be? Are the penalties supposed to be paid the day you pay what you owe or is it mailed to you? Does what you owe accrue interest even if you don't know how much it is?
I wouldn't worry too much about the federal filing because your spouse filed for an extension and you are to eceive a refund.
For the state (The $544), the answer to your question is really based on the state you live in which you did not provide. Suggest going to their website to understand the 'worse case' scenario. Then I would suggest just wait for the State to correspond with on whatever penalty make be required.