It's because Kairi's heart was within Sora... he senses a familiarity with the place, because this was actually where Kairi was from (eluded to, and is most likely fact). Sora also has the same feelings in Deep Jungle when he's watching Jane's slides... one of them is a picture of Hollow Bastion (oddly enough) and he gets the same familiar feeling.
It's the same in Chain of Memories when Sora uses the Twilight Town card... he senses a familiarity about the place, because this is where Roxas originated into. His heart knows the place, though he can't place it. In Hollow Bastion, Kairi's heart knew the place and it resonated into Sora's own.