Entries with timed scores can be very "sticky" once scored. Simply moving a scored competitor from scored to unscored does not erase their saved results.
To add a penalty to a previously scored entrant: Unscore the entrant > Press the "Save Scores" button to save your changes > rescore the entrant with the penalty/comment > and click the Save Scores button.
Saving the scores will erase the previous time/score and let the system accept the new score or comment.