If you watch Colonel Kira's baseball shirt from the beginning of the game with the Vulcans to the end, you can see that the name on the back of it changes from 'Kira' to 'Nerys' during the course of the game.
I don't know what her rank has to do with the slip up at all. But I saw that episode, and you're right.
It seems weird, first of all because Bajorans first names come last. Her family name is first, her personal name is last. So the humans get their last names put on their jersey, hers should have been Kira all the way through, which is her family name. I don't see why they'd even put her personal name at all.
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