This doesn't appear to be the same issue as the past one involved qualified maps as far as I'm aware. I think that might be what happened with the first example though since they last played 2 years ago.
I just managed to reproduce it and it seems to be related to the recent one-score-per-mod-combo feature.
I reproduced it by getting an A rank score with no mods, then getting an SS rank with a mod. This added an SS rank to my total and deducted an A rank. Using further mod combinations deducted further A ranks as I still had the nomod A rank score. As you can see I not have -2 A ranks and -1 S rank in CTB.
Seems to be a pretty big oversight that probably affects a lot of people without them realising, not sure how viable recalculating them would be with this many players though.