Exactly. If you look at the comic and the movie together they haven't actually done anything that is impossible in the Trek universe. A lot of stuff that is implausible perhaps, especially when it comes to character motivations, but nothing that actually goes against the universe.
That doesn't say much, given that pretty much everything is possible in the Trek universe. The only law it follows in the one of plot convenience.
ST has enough technobabble already. Did they REALLY need to introduce new stuff? Like that red matter and black hole time-travel?
They were tracking the launches and projectiles prior to the warp and had precise data for where to shoot on arrival. The fleet, on the other hand, went in blind and was engaged at extremely short range, as was the Kelvin. Boxer versus a puncher. The Federation ship will only have an advantage as long as it stays away. (Which given the more recent vintage of the Narada was probably impossible.)
That explanation doesn't hold water, sorry.
What's preventing other frederation ships from tracking the missiles from warp? How do you know the Enterprise tracked them prior to warp?
Also, they are missiles - they change their flight path, they don't travel in a straight line. So long-term prediction is pretty much useless here.
And finally, we have computers and radars powerful enough to lock on, track and direct fire on missiles within a second right now.
Federation ships shouldn't have trouble shooting down missiles the second they arrive.
EDIT: Come to think of it the whole "Spock should have been in shock about the Romulans" thing is a red herring as well. People aboard the Kelvin saw what Romulans looked like before then and I have to believe the shuttles would have saved some kind of "black box" of the transmissions recieved prior to abandon ship being ordered. They did know what Romulans looked like assuming they could identify the Narada from the same information as a Romulan craft. (Which apparently they could.)
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