I also have an Xbox controller plugged in and configured as a drone camera, & have never seen your issue on my PC, so I think that possibility is unlikely. I also have no 3rd-party apps running either, though.
I do occasionally see this type of error message when shutting down the PC in other situations (unrelated to MSFS) - hence my question. For example, I occasionally see it when using the windows disk cleanup utility just before I shut down the PC. However, your issue may be caused by something else entirely. 