If you have a flight plan defined, and you use the gear icon to the left of a waypoint to "Remove this waypoint" then it works as expected -- that is, it deletes that row in the list and moves all subsequent waypoints up one row. But not if you remove the first waypoint (usually the departure airport). If at any point in your deletions you remove the first waypoint, then from there on out the screen does not update itself to show the updated list with the waypoint removed, and any waypoint you remove from there on out also does not show itself removed. (They actually are being removed, which you can see by clicking on the Close button and returning to the map.) It's just some "boundary" issue with the list index/pointer.