I don't think it was simple. It came down to the odd specifics of scanf making the algorithm O(n^2) which wasn't obvious at all from the programmer standpoint. A lot of people pan Rockstar for being incompetent but in reality, it's a C footgun that any programmer would make.
Edit: I reread the article and I overlooked how there was a second issue of a poorly implemented "hash table" that was a linked list that checked the entire list for dups in every update. Since we don't have access to the source code, it's hard to say if this is poorly implemented piece of code on Rockstar's part or someone else. It could be some deeply buried piece of code that no one ever looked at for years until now.
Edit: I reread the article and I overlooked how there was a second issue of a poorly implemented "hash table" that was a linked list that checked the entire list for dups in every update. Since we don't have access to the source code, it's hard to say if this is poorly implemented piece of code on Rockstar's part or someone else. It could be some deeply buried piece of code that no one ever looked at for years until now.