You can use this class’s Channel Divinity twice. You regain one of its expended uses when you finish a Short Rest, and you regain all expended uses when you finish a Long Rest.

That’s the rule from the new “core rules” version of the class. Which version are you using, the “core rules” version or the older “legacy” version?

Core rules. Double checked Legacy is disabled under 'Sources'.

Oh, that’s because the system is incapable of tracking a resource over a long rest and partially restore the expended uses on a short rest. The system was built to be either/or, not  both.

That makes sense; however, why can't they then add 2 sets of tracking checkboxes or at, the very minimum, add a note to the character sheet, so player's are aware that this has to be tracked and updated manually during short rests?

To fix this in my homebrewed, corrected copy of the Oath of Conquest subclass, I created 2 separate Actions for the subclass feature options - one for short rest and one for long rest. Not ideal, but it works and I don't have to remember to manually uncheck the box when taking a short rest. Here's an example.

Barbarian's Rage has the same bug.