The CG people needed to work on their proportions. The shuttles were too large in relation to the rest of the ship in the scene they showed one docking. But in general, proportions and scale were the biggest problem of the movie. (Seriously, less than 5 minutes from Earth to Vulcan? Or the fact that everything in the Enterprise seemed to be only a couple of hallways away from each other? Or seeing Vulcan from Delta Vega?)
If you look at it, the saucer section is at least five levels thick, and each of those has to be at least 20' or so (for all the ventilation, plumbing, wiring, etc etc etc...). That means the saucer's at least 100' thick, and the main body was at least that thick, as well. That room would have no problem fitting.
Actually, in my opinion, they made the Enterprise a bit on the small side - or I'm misguessing the number of levels in the saucer section.