I finally found out the cause of Kodi’s consistent failure to add most new episodes. Only removing and adding the show again worked. It failed to detect new items because the modified date has not changed for the directory. Running the touch “directory” command fixes the issue. This happens even when you specifically scan for new content of a particular show meaning it is impossible to scan new episodes without first removing the show and then running a full library scan.
Why does Kodi work this way? Modified date does not change for directories when files are modified or added within a sub-directory such as season folder. This is easily avoidable if Kodi just scanned sub directories to see if modified-date is different on any sub-directories. This seems like a major bug to me or am I missing something? Is there a workaround?