You can request it from the IRS similar to a 1040. Enter the type of return and year in boxes 6 and 7 of the following link. There is an option for 941.
4506
When they say you owe, they are disputing that either the payment was not made on the amount due listed on the return or that the calculations were wrong to get to that total. The Self Employment tax was calculated wrong or payments made throughout the quarter weren't added incorrectly.
You will get to compare the payments made, payments due, to your bank statements to see if you actually made the payment.
