Yeah, reiterating on another comment, there was nothing confusing about it. The TV show universe is not real life. In the TV show, there are (or were) only 4 blue eyes in the entire world. Pegasus printed only 4. Kaiba destroyed the one Yugi's grandpa had so that it could never be used against him. Not only can you only play three of the same card, but you only need three blue eyes anyway to maximize its potential.

And He did the same thing with Exodia after Yugi beat him with it: He threw it into the ocean so that Yugi could never use it against him again.