The new autoscore has become an issue because it is scoring boards on the basis of hypothetical variations it sees, but that the players did not see, rather than scoring it as it stands. This means, in effect, that KataGo has become a third player in the game. This has the consequence that in some cases the game play information contained in the KataGo variation can help one of the players to alter the game result, which is a violation of site rules against players receiving outside help.
For more details, see Autoscore is still overriding players’ skill level