Usually there is a straight forward numbering given for the checklist items bundled within each checklist group container. Each newly added item increments the index value of the indentation level it has been added to.
However, there may be circumstances that lead to checklists that seem to have broken numberings when they are viewed or evaluated via the Checklist Viewer interface. If evaluators complain about this fact, checklist authors do not have to consider this a bug, but simply open the project with the Checklist Editor interface. If the missing index values belong to items that have an active condition option, their index value is missing in the Checklist Viewer by design.
Imagine the influence conditional items had on checklist item numbers if the index values were changed whenever the availability of an item is changed: The ID of all later items within the same group would change as well. This behavior would make it quite hard to refer to checklist items by their group and index value, which is why RayQC simply numbers all items independent from their current state of availability.