Huh? Sort of hard to tell if there's a problem if you remove the text about what happened.
I transferred a Marauder-flying character over yesterday, and I also did not have anything in my ship's hangar after conversion. I had to buy some fighters to put there. Since I chose the ship with a token on Holodeck, I don't have the option of deleting it and reclaiming to see if a new grab would grant something for the hangar.
Well, I have to revise my statement now. Turns out since today's patch, not only didn't I get any sort of fighter craft for my Marauder, its console switched to a hangar item, which as far as I can tell, is quite wrong. At least the console was a working power-giving console before, even if I had to buy fighters. Now putting the former console in the hangar (only place it can be slotted) means you can't use fighters at all.