@ Lissart.
Thanks for that very thoughtful set of language thoughts. I suspect a well-attuned native English speaker can even detect an intention to query rather than to confirm even from a flat, laconic mid-western US pilot accent!
IMHO, the controller was so distracted that she really didn't "hear" the read-back / query at all. If she had, then the twice repeated "Nine Right" should surely have alerted her that something wasn't right. The BEA report focuses on her initial slip of the tongue - 9R instead of 9L - but she then missed that slip being repeated by the United.