Part of this has to do with inevitable flaws in manufacturing. Nothing is ever totally perfect.
GPUs have many multiple identical cores running in parallel to achieve the processing power they do. But during manufacturing, let's say for simplicity that the GPU is designed with 64 cores. But in testing, only 57 of those cores actually function as expected.
So what are they gonna do? Well they're damn sure not going to scrap the entire chip, they just basically block out the bad cores and sell it as a lower end model with reduced processing power. I'm practically certain this also affects the potential bus width of the final product.