Same problem here. I'm not happy that I spent 2500 Zen on 5 fleet modules and now I'll have to spend another 2500 zen to buy the regular ship. Going to send in a bug report and ask for compensation.
Support confirmed this is a bug and elevated it to those who can fix it. I had a screenshot showing the Fleet Atrox and the error message saying I needed to own the Atrox in order to buy the hanger. I think because I had that evidence they compensated me for the error. Of course it could also be because I spend a ridiculous amount of money on the game.... ;-)
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AirBear