Just played around with this a bit and found that it's something between a visual error and a serious inconvenience.

If you select a group of notes, then drag and drop them, there's a chance they'll become unhighlighted. If you then scroll down and back up to the notes, they'll be selected again. This makes it seem like the notes are "ghost-selected", but that's not the case either. If you drag and drop the notes, then try to move one note as if the group were still selected, only the single note reacts.
You can also create a bunch of different weird interactions by scrolling to view only parts of the selected group as well.

So scrolling fixes unselectable notes, but it's enough of an inconvenience and causes enough confusion to warrant a PR from one of our coder friends (much appreciated!).

The yellow notes in the note preview playhead are the ones you currently have selected.

Ah, I see, sometimes you can make a selection, it selects the notes, but doesn't create the boxes used to drag them around????

I can't figure out a way to always recreate it, sometimes you do something and it removes the selection boxes from your notes but keeps them selected and deselecting and selecting them all again doesn't bring them back, however individually selecting the effected notes properly creates the selection box.

That said though, it doesn't effect the event selection, which might help pinpoint where the issue occurs.

Wait, I've just figured out a method of recreating it - end your selection over a note when you move it and put it back at the same position:

I guess I just wasn't paying enough attention to the video in the description.

Also, undoing restores the selection boxes, which is nice to know.

Ok, I might have figured out a fix?

This issue now has a pending PR. (Yay! I fixed it! I thought I wouldn't be able to fix this)

Also, this issue could use a rename to better reflect how/what causes the issue to happen - moving the notes but returning them to the same position and releasing, causes the selected notes to lose their selection boxes.