Seems to only happen sometimes, made me double take but this time I'm 100% certain. I fill my own Guild Ship with Level 15 Witch Doctors from my second island. Other than that I had Level 30 Gunners in the Guild Ship. But at the end of the game I see different troop levels (that match my own troops actually).
The more I pay attention to it the more I notice this problem. Now I'm second guessing myself - has it ever shown the correct levels? This screenshot shows the bug in all its glory. Two lots of Level 33 Gunners? (In reality I had 5x29 and 1x33 from memory, and the Witch Doctor was Level 15)