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The following contains minor spoilers for Finding Dory. You have been warned!
One of the most fun things about going to the movies is going with people and then discussing the film afterward. This can also be one of the most infuriating things. We all have different experiences that we bring into the theater with us. This can be fun when somebody brings up something interesting about the movie that you never realized, especially if they have specific knowledge about aspects of a movie that you do not. Of course, these people also tend to be a little hypersensitive to those things as well.
Such was my experience seeing Finding Dory with my wife. She really liked the film, but, while she likes enjoys movies, she's also a professional biologist. This means that no movie that contains animals of any kind will ever escape her eye. Finding Dory was no exception. Overall she loved the movie, and thought that they handled their aquatic facility very well, and since it's an animated movie realism mostly gets a pass, but in reality, Finding Dory would have a few problems.
Dory's Parents Would Be Dead
Dory and her parents are blue tang fish, which is a type of Indo-Pacific surgeonfish. This means they live in an area of the Indian and Pacific Oceans, around Indonesia, Australia,and the Polynesian Islands. The water off the California coast is far too cold to suit the species. Even if Dory herself could handle her short-term exposure to the colder water (and it's unlikely she could), her parents, who have been living there for years waiting for her, would have perished long ago.
Beluga Whales In Morro Bay
For those of you not up to speed on your California geography, Morro Bay, CA is on the coast, about 100 miles north of Santa Barbara. It isn't quite "Southern CA," but it's pretty close. The beluga whale, on the other hand, is an arctic species. It lives at the extreme north of the planet. There's little reason for a marine center in Morro Bay to have a beluga whale. While there are a number of beluga whales in captivity in a number of places around the world, not all of them arctic, as the film's location is more than simply an aquarium, someplace closer to home would be a better fit for research and rehabilitation. Someplace like the Vancouver Aquarium in British Colombia, which already has a pair of belugas. They're actually thanked in the Finding Dory credits, so obviously Pixar got their information on belugas there. It would make more sense for Bailey to be there.
Saltwater Fish in Freshwater
Of all of the issues that Finding Dory may have had, this one may have been the most obvious. While Dory, Marlin, and Nemo are saltwater fish, they spend an awful lot of time in fresh water. Now, it is possible for saltwater fish to survive in fresh water for limited periods, assuming the temperature and Ph levels of the water match, but Marlin and Nemo spend a great deal of time in a gift shop aquarium, before they finally escape that to bounce off water jets that are likely also fresh water. Even if being in that water didn't kill them, neither should really be feeling very well after the ordeal.
Bioluminescent Squid Need To Be Deeper
Near the beginning of the film Dory, Marlin, and Nemo, are attacked by a massive squid after being told to be quiet by a bunch of crabs on the seafloor. A massive bioluminescent squid. Bioluminescent sea creatures live at extreme ocean depths. This is why they have the need to be luminescent. You can't see at that depth without your own light. The crabs, on the other hand, couldn't survive at those kinds of depths. For that matter, neither could Dory or her friends. Since Dory hears Sigourney Weaver's voice immediately after, we know they're not that deep, that means the squid is much too shallow.
Whale Echolocation Doesn't Work Outside of Water
Many animal species use echolocation to get around, and whales are just one of them. However, one caveat of whale echolocation is that it requires the water in order to function. It's the movement of the sound waves through water that gives the whale the information it needs. However, every time Bailey the beluga uses it, he's half out of the water, and the half that's out is his head, the part that makes sounds. Even when he uses it on the pipes to help Dory in the water, his head is out of the water. He would have been utterly useless in that position.
The Open Ocean Exhibit Is Not Open
This one is less of a biology problem, and more of an aquarium problem, but the Open Ocean exhibit seen in Finding Dory is not an open ocean exhibit. It wasn't open. The exhibit has a massive rock face and it's full of kelp. There's little open about that. Granted, an actual open ocean exhibit is nothing but open water and swimming fish, so it may not be nearly as eye-catching, but all they had to do was put Dory's parents in a different exhibit. If they had called what we saw anything other than "Open Ocean," it would have been just fine.
Whale Shark Eyesight
This one isn't really a problem with Finding Dory. Instead, it's a joke that only a biologist would get. The running gag regarding Destiny the whale shark is that she has terrible eyesight, she's nearsighted, to be specific. The truth is that whale sharks can see just fine, however, as the largest fish in the ocean, the whale shark actually has incredibly tiny eyes as compared to the size of their body. So, Pixar wasn't just giving Destiny a random affectation. It's actually a whale biology joke that most people would never get.