The falling from space scene would have to be in the middle of the movie when they first get back to Earth with the other ship(among others no doubt) crashing into the bay and various buildings blowing up. Hence why they would have to go to Q'onos to capture Harrison right after in
this little ship instead of the Enterprise. Clearly it now seems that the term "detonating the fleet" is actually literal as first thought. I would bet that Harrison got the prefix codes for the ships around Earth(or any that would be in range) and synced it with the explosions on Earth. Some have mentioned that the damage does look like the kind caused by internal explosions and they could be right except for the scortch marks which im guessing are from the volcano resuce of Spock. Kirk(?) in the space suit avoiding the debris with our(?) moon in the background could very well be the same scene. What would Kirk be doing outside the ship leaving Spock in command I don't know.
And once they get back from this mission they find the Big E waiting for them(with minor changes at most!). The new girl is not going anywhere anytime soon. Logically its waaay too early to bring out a massive refit let alone the "A". Its only been a year if that after the events of the first. Come on peeps use your noggins lol.
And I would agree that the ship crashing into the bay and the one taking out buildings is the same one.
Then there is this place
here. Looks like a massive starship armory or something. There are atleast three bays with what could be photon warheads and others with probably matter/anti-matter storage pods and such. A few seem to have some small ships(cargo ferrys?) which would explain the tunnel.
erk one issue with that thought process... the ent rising from the water isn't damaged...
...and takes place early in the movie.