Whenever I look at the species chart, it just shows the same fish in all 7 locations, even for the ones I've breed. Is this some glitch or do I have to buy something in game to get it to work?

The species chart will show the same species of fish in all positions if you've gotten that particular fish from eggs, or if you've bred the same species fish together. I haven't ever seen a problem with the species chart when different species are bred for at least 2 generations.