When you choose a source folder for your Publish post, Publish only adds the photos directly inside that folder. To include photos from folders inside it, turn on Import images from subfolders.
How do I include photos from subfolders?
To include photos from subfolders in your Publish post:
Open Preferences. Press ⌘, or choose Preferences… from the app menu in the menu bar.
Go to the General tab.
Under Import Subfolders, check Import images from subfolders.
Note: With this on, Publish adds the photos from every folder inside your source folder. The setting applies to all your posts, and it's off until you turn it on.