Yes understood about no-shows and people not checking in at all but not a system that allows you to check a person in twice unless ground supervisor or equivalent 'forces' them in the flight after several checks.
The worry if it becomes common and complacency kicks in that one day a flight departs without somebody on board who should be and carrying the content of their luggage.
If as suggested by an earlier poster the system allows check in twice, I suggest a fix must be found esp as they seem to suggest its happened numerous times lately ?