Based on what I see, the problem may be that the stump is serrated, as are the levers. If they are close to one of the serrations, the teeth can lift the lever up, so it does not leave a mark.
On those, I find it easier to move the bolt back a little bit, then install the levers with the stump in the proper gate. Then you can cut the key bitting to fit the levers.
That may require filing down the part of the key that moves the bolt so the key can turn past it, allowing the levers to mark the blank. Then, when your key bitting properly matches the levers, copy the key to a new blank, so the part of the key that engages the bolt is back.
Gordon