Here is the thing you're sort of assuming Xehanort was saying both the people on his list were vessels and that's not what he said. What he said is that two of the people Mickey listed belong to him. By stealing Sora he stole Ven, both of them at that moment belonged to him, and thus neither of them could be a light even if only Sora was able to be a vessel it keeps Ven's heart from being able to be returned.
Also I'm pretty certain Xehanort is more than aware of Ven's heart being in Sora. He's basically a genius and would have likely realized it the moment he saw Sora's Nobody is Ven's twin. He probably could also sense Ven's heart inside of Roxas/Sora or heck seeing as he scanned Sora's memories in KH1 it's quite possible he learned right then and there what transpired. Of course the fact Vanitas is also Sora's twin also is pretty good indication, and Sora having two keyblades is even more evidence. Really there are so many signs screaming it and Xehanort is one of the few people to have seen all the signs it's hard to imagine he couldn't put it together. Especially since fans had put it together long before BBS was even out.