Just started a quick game and purposely did nothing but get to trading. For my first level up on city I even picked Fortress to make sure that the bazaar isn't a Town only building. Didn't build a merchant in that town even. As soon as I hit trading Merchantcross Bazaar is available to build in that city.
Another possible reason you can't build is lack of space possibly? Are you surrounded by swamp tiles in that city? If so, you'll need to raise land on some tiles to create some more room for city growth. If not that, I'm not sure. Oh by the way, this game I played with Tarth, didn't want to have monsters coming in and wrecking my quick game
Is it possible certain races can't build this? I usually get this building built, but I play primarily with men and not fallen. Pariden, Altar, and Tarth are my most played, and I have definitely built it with all of them.