I have this set and it does the same thing for me. The problem is that the size of the model and the tolerances between bricks add up and by the time you have a structure of that size not everything fits perfectly.
First thing you should do is make sure all the pieces are properly seated all the way down the construction of the model. It is possible to make the pieces rest in the proper position.
If that still doesn't work for you, you can certainly fix it by replacing some of the tiles with plates. The building is meant to be modular, and thus easily disassembled into sections, for play/display purposes. If you rebuild it with plates instead of tiles it will have more structural strength but will be more difficult to disassemble.