Hi Tina,
I would go for the 'manual' process of creating your credit note transaction. That is, entering a line with a negative quantity, as you wrote above.
The credit note functionality should actually not do something else but maybe a problem with your IC-Transaction occured that messed up things.
To be 'safe' - and against the background that you can't replicate the issue - I would thus recommend the manual way.
Best regards,
Ludwig