But then, there's all kind of things they overlooked.
I always wondered at exactly what point Marcus and Khan stopped being allies. By extention, I wondered why Khan beamed to Kronos at all.. was he personally interested in having the Federation start a war with the Klingons? These two questions seem unconnected at first, but once you look at the plot, story, and details, you realized that certain plot elements were not worked out.
Also, I know that 72 was the number that the writers had been handd on a silver platter from the original episode, but it's an ungainly number. It would require more torpedo launchers than the Enterprise has (until the CG people had aplaced a few on the side but not nearly enough) and it was too much for Spock to have people take out the cryo-tubes and install explosives.
I watch the film for the performances.