First - I tried to submit an ingame ticket for this, but for the life of me couldn't find a way to do so for a ship.
I just got my Starbase to Tier 1, the Shipyard built and the initial Provision run completed. I then had a Scourge Destroyer Retrofit constructed, and it shows up in my ship list, and is selectable as my current ship. All good so far.
I then went to the Ship "Tailor" in Qo'noS Shipyard, and as soon as the screen opens I am faced with a cost of 1500 Zen! Haven't changed a thing, or even touched any selection.
I them tried to change the color scheme to Lacerda, and add the Fleet insignia - the list of color patterns is truncated at about halfway, and the KDF/Fleet option doesn't even appear.
I have two options - blow away the ship and re-build her (I have enough FC for this, and the Shipyard Provision) - not my first choice - or hope you can fix it.