either the in game lore was false or the universe is a different universe where plasmids were actually discovered some other way
Well maybe the vigors will be the something invented in space by a mad scientist and then the whole space station blows up and then the stuff gets sunk into the ocean and all the stuff like adam and whatnot gets rediscovered years later at the bottom of the ocean and they rebuild a station down there to save humanity and then Bioshock 1-2 happen. But it's not a prequel because even though its the same universe, the people on earth don't know about what's going on in the sky so the stuff gets rediscovered and all the people on earth think that this stuff is really from the ocean.
Or something... the point is, they can make something up to explain "holes" in the lore. Or, they just created a game that has a different story and reused what they already had and called it something else. I guess that would be cheap, but I find the gameplay fun anyways and you can see games games doing that all the time. Madden releases a game every year that basically is just a roster update, and Call of Duty releases the same game every year so it wouldn't be something new for a game company to do. Names sell, and since it has the Bioshock title on it, it will sell and I'll buy it. But not because of the name recognition but because from the first 15 minutes, even if its not the same universe, the game looks awesome.