I am not typing in any sprite names. This is all being done in the editor, so there is no room for typos. When this issue occurs, many of the widgets seem to default to the first sprite on the atlas.
The reason for the term Atlas Reference(s), is because I have 4 different Reference Atlases I am using, since I cannot fit all my assets onto one atlas. I am using references so I can at run-time switch between SD, HD, 4X. This issue happens whether I have 1 or 10 atlases though, so that's not relevant. I am not changing anything on the widgets themselves, but many widgets will end up defaulting to the first sprite on the sheet in certain scenarios when the Reference Atlas is set to null.
Edit: I should add that when I said sprite references earlier, I was meaning the sprite name that each widget is set to.