Just out of curiosity I checked where Heroic Leader is and it is not in Bremenhaven yet:
https://www.vesselfinder.com/vessels/details/9441570
That said, they probably decide which cars will be loaded before it even docks so that is what you are seeing.
Actually, I called a Genius and a) he confirmed you may be marked In transit with a specific ship before it even docks, and b) the At Port status on the website should actually be "At port or compound" and that my car was not scanned at Bremenhaven entry yet. So it is either still traveling to port or not being scanned as being at the port yet.