the fact that they didn't use animation to show the decoding, instead, we got a tv-esque sound effect for when he is "decoding". The movie A Beautiful Mind shows us how a genius decodes in 3D, filling the room. What a lack of foresight not to come up with this themselves.
shareHave to admit I've just watched this again and was almost half-expecting a Matrix-style effect every time Simon looked at the code.
That said, I think it would have been a bit alien compared to the rest of the film. While it is 1999, other comments below suggest the movie does seem slightly more dated, and randomly animating that coded page might have seemed a bit out of place.
On another note, think it was a bit harsh for Willis to receive a Razzie for this...