Did you start with a clean sheet design or did you use the transport as a base? There is a bug where the ship icon doesn't update properly when saved if you change an existing design.
I always obsolete the auto designs and didn't have any Transports when I made the first Carrier.
The Carrier template uses cargo hulls. I started with a large hull.
It happened again with huge hulls. All of my Carriers look like Transports, but the AI Carriers look like Carriers.
My other ships look like Scouts, but the AI ships look normal. It seems to be a problem with the Krynn.
This is the first game I started with the 1.12 update and my first time playing as the Krynn.