When a new issue is created, there's an option to link it to an existing epic via the Epic Link field. In this case, there're chances that the issue is mistakenly linked to a Done epic, which will then make it invisible in Plan mode of a Scrum board when the Epic filter "Issues without epics" is selected.

Suggestion is to hide Done epics or make them unselectable from the Epic Link field so that new issues can only be linked to active epics.