Well, I called it, didn't I?

The crew of the ship were running around while Georgie was on a higher level of the ship with a young girl. Before the dragon came, the scene consisted of Lucy having a conversation with her. When the dragon does come Lucy ducks down and forces the girl down with her, but when the ship’s crew start to fire at the dragon when he’s on the mast, Lucy shouts ‘what’s he doing?!!!’ or ‘what are are they doing?!!’ or something like that, obviously she is not happy with the fact that the dragon is being shot at.

Previously I wrote:

Eustace gets turned into a dragon. Not being the brightest kid on the block and perhaps not thinking through what kind of reaction the DT crew would have to his appearance, he flies to the ship and is very surprised and taken aback when he's fired at and injured. Disappointed and a sadder but wiser dragon, he flies back to the Island.

In the meantime, Lucy got a good look at the Dragon while he was at the ship and can't shake the feeling that something is up. She recognizes that he wasn't trying to attack them, and feels awful that he was injured. She convinces Caspian and Edmund to put to shore so she can try and heal the dragon's wounds. There, they meet the dragon face to face and Lucy is able to discern that he is, in fact, Eustace.

I'm even more convinced that this is going to be the case.

I like your theory, Gymfan, but that still doesn't explain why everyone is on the ship, and obviously not Eustace. I think that they haven't kept track of everyone and they think that Eustace is on board. Or maybe they have already fixed the ship and are getting ready to set sail, when the Dragon attacks and then flies off. Then Lucy realizes that Eustace is missing, and then they go back to find him, or rather the Dragon.

Has the idea that it's only Eustace's fantasy that he's attacking the ship been discussed properly?
I can't believe they would be sailing off without him, since there is so much in the book looking at that whole issue - Lewis is adamant that Eustace is wrong to think they would go without him.
Even when they know he is the dragon, in the book, they try to think of all possible ways to take him with them.

I don't think they're sailing off without him. I think they went back to the ship to re-group, discuss search methods or figure out what's going on (it could be a case where one group things Eustace went back to the ship and the other thinks he's still on the Island, so they ALL have to go back to the ship before the error is discovered).

Eustace, not being a nautical person, might see them all on the ship and thing they're leaving, and fly over in a bit of a panic without thinking through what an effect his sudden appearance might have on the crew. Then, wounded and bitterly disappointed, he goes back to the island, where he's eventually found by an insistent Lucy.

I think there are a bunch of scenarios that could get the whole crew on the DT without them actually preparing to sail off.