Earlier, when I undocked on my Kempeitai ship to go on a short patrol, I noticed that about half the textures on my Tora HF were the same as the ones on the KNF Chimaera HF, as seen here:
The textures displayed fine yesterday, and the mod hasn't been updated since then, so I docked at Shinagawa Station to test a theory. When I undocked, everything was fine, confirming my suspicions.
This is caused when two different ships share material names. Both ships display the first material by that name loaded, even if the game's files reference a different MAT. I suspect somebody got careless when cloning the KNF line for the Exiles and didn't properly rename all the materials.