Transiting somewhere is not a visit nor is it residing there, even if you need a transit visa.
You can list it as part of the trip description, but it's not a destination she visited, so it does not seem essential to do so.
IRCC does not have access (without explicit approval) to CBP records. If those are requested you'll be asked for more information, so can clarify at that point. And moreover, if those records are requested they will indicate that this was a transit visa, likely with an entry and exit on the same day.