When I select a captain's yacht as my default shuttle, I am referred to by NPC as commander of the [shuttle name], not of my proper ship name. They are referrring to my ship as the shuttle name, even though I am commanding my cruiser at that moment.

I concur with this report and other posts like it. I put in a bug ticket detailing the same problem, and interestingly enough, it started with my captain's yacht, but now extends to all my shuttles I tried switching over to my yellowstone; same problem. I tried selling it while active; it switched over to next shuttle of the three I had which was my timeshuttle; same trouble. I think it isn't specific to the yacht, however. This is likely a bug coded into the new ship selection system.

Strangely enough, when I switch to my other starships, the glitch isn't present, but when I go back to my Vesta, the bug resumes. I wonder if I should discharge my Vesta and reclaim it and see if that works...

EDIT: Nope, doesn't work when I tried to reclaim and switch to my vesta. I have the 3-pack, and tried claiming and switching to each one, and the bug persists with each one. I'm now convinced it's connected to the vesta line of ships themselves. It started with them for me, and it continues to persist with the vestas, and only the vestas.

Is this happening for others on different ships?

The same thing is happening on my Blockade Runner Escort Retrofit: Steamrunner class.

If I go back down to my Captain Level Intrepid Class or any other previous ship it displays correctly. Everything I have Rear Admiral or above (Prometheus class Advanced Escort, Mirror Assault Cruiser, Mirror Science Vessel, it displays my Danube Runabout. I had thought it was only the purchased Retrofits and lock box ships, but my Prometheus Class is the odd one out because its all standard, non-retrofit, no multi-vector assault module

It's not just ZEN ships. My ship is now the Tribble Killer--which is the name of my friggin shuttle.

Happens with my Nebula and the Vulcan Tal'Kyr support shuttle to both Zen and with my Galaxy and standard shuttle both have now decided to share identities!

I also have this issue with my mirror star cruiser, my ship info shows my shuttle as the ship I'm flying as well as the shuttle name on my info tab. When I look at other players info who are also flying mirror ships I see the same thing- their shuttle type and name both in space and on ground.