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.
https://www.youtube.com/watch?v=UsmqWSZpgJY
But this is online GTA. I can imagine that they handed it off to another department that didn't have the same amount of discipline and expertise. it's probably an off shoot team that creates content for the engine but don't necessarily need to dig down into how the engine works.