Credit has always been and will always be dependent on the booking class and not class of service. While perhaps unintuitive, there are many airlines and booking classes where the lowest business does not earn anything. For example, Lufthansa P-class is notoriously earning nothing with many partner airlines.
I am pretty sure there is a disclaimer somewhere that will state the calculator is not a definitive source of information, and earnings can also change between booking and travel.
This sucks for sure and you can always come to this forum to validate that flights will earn. I highly doubt that LH will do any adjustments due to a mileage calculator readout from last year.