Why does config, save and intermediate wreck my games?

As I build up my game over time the config, save and intermediate project folders slowly grow. It got to a point today where it corrupted the game to getting a bunch of nullpointers and I couldn’t click the level blueprints button on a completely empty level. Why would these folders corrupt a game and make it crash even on completely empty levels when nothing gets loaded? Not only that but once I cleared out the folders the game got exponentially faster, I don’t get why these folders are growing automatically, slowing down the editor and then corrupting my game.