This might be a blind leading the blind.. cuz i don't really get it either.. but i assume that since mc forcefully made the bond while the rock was unaware.. it caused negative effects since the rock couldnt help them... And then the only way to stop it since it got worse real quick.. was to sever the bond that was never meant to be... I think..?
what i think is that since the mc tied a forceful red string with the ml, it obviously had negative effects on the ml (who’s supposed to remain un-bonded), and now, it’s trying to end that bond between both of them. according to the story, the only way to get rid of misfortunes in a non-bonded soul’s life is to end the forceful bond they entered in(which i have no clue how it happens, or maybe instead of ending the bond, simply keeps them away?), and maybe thats why the memories of the ml were taken, because the mc and ml loved each other so much that if the memories would have not been taken away, they would continue loving and staying with each other, which would in result leave the girl(who is originally bonded to ml) alone(in means that she would not be with her destined partner)
but this is all i could make out of the rock’s doing :p
I think what the rock did wrong here is to fall asleep and could not stop Yeon when he forced the red string on Kihoon. However, the rock wants to help them find happiness, in order to do that the forced bond has to be ended. The purpose of the ss2 quest is to remain “the clear status of the red quest” that Yeon and Kihoon achieved in ss1 even if they regain the memories of their past lives. However, Yeon has failed the quest, he knew that because of his doing Kihoon had to suffer all the misfortunes, so he wished Kihoon to forget all of it and start over. But the artist said ss2 is rather a gift, also the rock mentioned that the solution is start fresh and connect the threads anew, which means after Yeon wished Kihoon forget everything, their forced red strings disappeared, it is an end to all the consequences of Yeon’s doing in the past live and is the begining when the rock connects their threads anew. Thats why Kihoon continues to fall for Yeon after 7 years.
Also to just summarize it. Our dummy Yeon could've already been naturally tied with Kihoon, it's just that forcing fate with the rock's red string breaks its whole nature.
The rock already forgave them after the first season, it was just the second that it wanted them to choose if they want to keep their memories and live with the burden or start anew

And explain what on earth the rock did wrong??? So the rock basically forcefully bonded them together or something?? Or cut off their red string??? I don't get it at all, why is there misfortune TT^TT