I had this on 1st attempt - 2nd attempt, I ignored ATC and didn’t change my XPDR code when asked initially. From there I was able to complete the flight by responding to ATC when the mission status prompted me to.
I think there are two separate ATC implementations clashing, the standard ATC for free flight and the ATC for the mission. I’ve found interacting with the standard ATC in a mission causes issues and the stages don’t complete correctly. I simply press the respond to ATC button when the mission dialog box tells me to.