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I also noticed that sometimes ships can't be deployed to specific fleets/locations. No idea why. Seems you can fix it by restarting the production line (obviously no good if its a big ship which has had production sunk into it).
Production menu sometimes is bugged when the game is not paused. Couple of times when I was selecting Infantry Equipment II, game was somehow interpreting it as Support Equipment. When I paused the game, it finally took my correct input.