Let us start at the beginning of the movie. This will provide context for what occurs later on, which is what you really asked about.
When the children get off the boat and step onto the pier, they are greeted by the site of a tram which takes them to the main concourse of the park:
They take this tram, you guessed it, to the main concourse. While there is no good, clear shot, this appears to arrive at the back end of the concourse as the very next scene shows passengers disembarking the tram and taking an escalator into one of the hotels.
This means that the dock is not by the main concourse nor by the hotels where the epic dinosaur battle at the end of the movie takes place.
At about 1:25 into the movie, a mob of park guests bust through a door from the main concourse into a back passageway, running from the remaining pterodactyls. The crowd is leaving the main concourse where the final battle scene takes place.
The children stay with Claire and Owen. During the Velociraptor chase, the children are in the back of the van that Claire is in, parked by the Velociraptor paddock. They do not evacuate with the rest of the crowd for whatever reason.
After the Velociraptor chase scene, we see that everyone is evacuating. The staff in the control center are evacuating: we see Dr. Wu being told to leave, and the other staff packing up and getting ready to go.
The park guests appear to have been herded somewhere else:
While it is not very clear, this looks like it could be where the children got off the tram earlier and went into the hotel. There is a tram loading dock next to a very tall building that is likely to be a hotel.
This is also where we hear the announcement about the next ship leaving in 45 minutes.
This shot is clearly at night or at least evening, and occurs after the Velociraptor chase: even if some guests were evacuated, there were still quite a few left as the dinosaurs were making their way back to the main concourse.
Next, we see what appears to be a shot of somewhere inside, perhaps the foyer of a hotel. Looking carefully, there is a zig-zag wall on the right which matches the zig-zag exterior wall in the shot above. This seems to indicate that the guests are in the entrance of the hotel, waiting to take the tram to the dock. They are likely waiting until the ship arrives in order to avoid being out in the open with vicious carnivorous dinosaurs on the loose.
Based on the sequence of events, it appears that as soon as the pterodactyls attacked that the guests were being evacuated. However, that many people cannot fit on one or even two ships: it took multiple ships and multiple trips.
Yes, the Indominus Rex and the Velociraptors were loose during the evacuation and the crowd was not yet evacuated: basic logistics says there is not much to be done about that other than to try to get those ships going as quickly as possible and to contain the loose dinosaurs as quickly as possible.
However, there are two very important things to keep in mind about what the dinosaurs are up to and how the humans are reacting:
The two park leaders are both dead at this point, and everyone else is fleeing for their lives. While Owen and friends are surely concerned about saving any lives they can, there is not exactly anybody around to "think of the children" so to speak. The crowds are mostly on their way, although clearly some park staff are looking after them. Everyone has to leave on the ships anyway, so the staff may as well do what they can to help the crowds in the mean time.
One would expect the Indominus Rex and the Velociraptors to take advantage of any opportunity (meal) that presents itself. However, they already have their quarry: Owen, Claire, and the children. Essentially, the dinosaurs are on the hunt for whomever was there during the initial attack on Indominus as well as any other scents they picked up during the ensuing chase (i.e. Claire and the children in the van).
It would not make sense for the dinosaurs to go after the crowd, even if they are sitting ducks: they have a score to settle, and the crowd is not within sight or smelling distance.
Once the fight is over, there are lot of guests recovering in what appears to be a hangar on the mainland (soldiers are keeping guard) the next morning. Clearly, a large number of guests must have been evacuated during the night.
Finally, one little nitpick. The control center is not on the main concourse. The research labs were, but the control center is a short distance away as this shot of Ms. T. Rex greeting the sunrise with some jaw stretching shows:
She is standing on top of the roof of the control center, on the helipad, looking toward the main concourse; we can see the hotels and other buildings in the distance.
All screen shots are from the Blu-ray release of the movie. They are copyrighted by Universal Entertainment and used here under the fair use provision of the U.S. Code.
