I've seen this issue several times in my years with Marriott and now with Hilton.

The issue is usually that either the night auditor checks the guest in after the night audit is run and then does not manually post the room charge for the day that is now past causing a two night stay to only get billed as one or the first night is manually posted correctly but the posting date will have the same date as the next night's room charge. In scenario B, it's out of the property's hands. They cannot credit a member's account a night's stay credit, only the parent company can do that. The software involved does indeed glitch on two charges for the same room on the same day.