Orphan files are not actually orphans

My graph view shows a few attachments (pictures) as orphans when they are not actually orphans:

One of the “orphans” here is referenced as follows in one of my notes:

Is this a bug, or am I missing something?

Does the image render properly in Reading View?

No. It is not just the images though, a whole chunk of the notes is missing in the reading view.

There was an embedded LaTeX equation above the images (i.e. specified by $$s) that also wasn’t rendering correctly in the reading view. Basically the whole section following it was gone under that section.

So, instead of formatting the equation like this:
$$
[equation goes here]
$$

I formatted it like this: $$[equation goes here]$$

And the problem was resolved. Everything is rendering correctly in the reading view, and there are no orphans anymore. Thank you for the tip!