When Yuri first leaves Ropesk, he tells Nia that he does not have any family. It is only after acquiring a ship and preparing to leave the Ropesk sector that Kira appears in the plot.
Until very close to the end of the game, this inconsistency is not mentioned. However, it is revealed close to the end of the story that it is not an error in the writing or dishonesty on Yuri's part: Kira was hastily created as Yuri's tracker by the Overlords only after Yuri left Ropesk, and false memories of their history were implanted into both of their minds. Yuri's and Kira's belief that they are siblings is not a direct result of the Overlords' manipulation but rather their minds attempting to "fill in the gaps" in the hasty story that the Overlords created for them, and this explains the inconsistency between their view of each other and what everyone else sees of their relationship. Genetic testing by Gavril Minas confirms that they are completely unrelated.