This is still occurring as of today. I just purchased a Fleet Escort and went to customize it. Without selecting anything else, I went to change my bridge and as soon as the window opened, it had 200 Atari Tokens in the cost.
This happens constantly on my Fleet Escort. Every time I want to change the layout from "Medium" to "Small" it throws in a 200 Atari Point fee.
After that, everything I do with interiors splashes the 200 Atari Point fee right back on until I log out. Problem is, half the time I change from one bridge type to another (that are already unlocked or free) it says it's going to charge me 200 points, no matter what ship I'm on (Fed side anyway, my Klingon ships have so little customization I don't bother).