I understand that actually seeing the events and practices documented in the movie can make a person reconsider and re-evaluate how animals are treated, including aquarium animals.
And that's probably what led you to ponder whether we are morally wrong for having fish in aquariums when we know it is not their natural habitat. No, I don't think it's wrong to keep them outside their natural habitat.
However, it does make me sad to know many live in bad unhealthy conditions, suffer and die. I don't read the "unhealthy fish" forum anymore, it's too sad, in part because most, or maybe almost all of it is preventable.
If anything, we may be morally wrong for not insisting that the whole industry from breeders to stores to ourselves improve how we treat and care for our fish.