So I have no idea how this happened, but just now I wound up with a second input caret that isn’t part of the whole multiple cursor functionality thing. It just sits there, blinking soullessly at me, regardless of what I do with the normal caret. An GIF:

Note that:

• it doesn’t move or alter text the way it should if atom was in multiple cursor mode.
• Adding to the start of the phantom cursor’s line does not increment the caret position.
• moving the real caret over the phantom caret does not clear it.

Switching to a different tab and back again cleared it for me.