A run out off a no ball can be scored in two ways, depending on the Auto End Ball (Runs Scored) setting, so please check this before reading the below.
If this setting is ON, then Wicket must be clicked first, as clicking the No Ball (Runs) value would just score the no ball and any runs off it, and complete the details as usual. However, untick the End Ball (0 runs/extras) checkbox before clicking OK, otherwise just the Wicket will be scored:
The Wicket button will be highlighted, and the No Ball (Runs) value, including any completed runs, can now be clicked to score the runs and end the ball.
If the Auto End Ball (Runs Scored) setting is OFF, the run out off a no ball can be scored as above, but as clicking the No Ball (Runs) value will not end the ball, End Ball will need to be clicked to commit the dismissal. However, in this mode it is also possible to click the No Ball (Runs) value first, as this will not end the ball, and then open the Wicket dialog and enter the Run Out details. In this situation, End Ball (0 runs/extras) must be unticked if there were completed runs, otherwise this will revert to a No Ball (Runs) value of 0, and End Ball will still need to be clicked to commit the dismissal.