Missing trees on Bookmarks tab in Safari

The side panel... meaning the Sidebar?

The icon circled below shows and hides the Sidebar.

Once shown, the Sidebar can show Bookmarks, Favorites, Tab Groups. Bookmarks are shown in the example below.

If a Bookmark contains subfolders they are indicated with the > to their left. Clicking them reveals their contents.

Describe what you're seeing that is not expected or is not behaving correctly.

Organizing Bookmarks is accomplished in a number of ways: Bookmark websites that you want to revisit in Safari on Mac - Apple Support describes them.

That's a Tab Group Favorite. You can edit them with Bookmarks > Edit Bookmarks.

Edit and customize Tab Groups in Safari on Mac - Apple Support

Of course I understand this may be new behavior for you, but I no longer recall how Tab Group Favorites appeared in the past, or how editing them may have been accomplished then. It doesn't seem abnormal to me though. Click Tab Group Favorites in the screenshot you posted and determine if the tree structure looks familiar. If so we can fix it.

What happened to my trees on the bookmark tab?

I am not sure what that may have been, but terminology can be confusing. We generally discuss Bookmarks in the context of the Bookmarks menu, or their presence on the Favorites bar, or the Safari Toolbar, or the Sidebar, or on your Start Page, but the presence of trees on a bookmark tab isn't gelling with me.

Perhaps Customize the Safari browser window on Mac - Apple Support will point the way.

Agree...backwards step when you many bookmarks and use sub folders.