Hera docks the Phantom nose first with the Ghost. Later Ezra, Chopper, and Zeb are working on it, and the view out the window shows a view facing out from the back of the Ghost. Then when Hera and Sabine depart, the Phantom is docked nose first again.
After Hera and Sabine load 2 crates into the Phantom (a green one and an orange one), the passenger compartment is nearly full. There are still at least 4 crates remaining, all orange. Hera then reasons that there were more crates but some were dragged off by local wildlife, raising the question of how they planned to transport all of them in the Phantom shuttle and why they wouldn't have brought the Ghost cargo ship. They finish loading up the available crates but there are only 2 crates seen inside the Phantom, both orange. When they unload the crates back aboard the Ghost, there are only 4 crates total, 1 green and 3 orange.
The Ghost hooks the Phantom from beneath with magnetic locks and takes off with it. The crew is somehow able to unload the cargo from the Phantom to the Ghost with the Phantom still locked to the Ghost's underbelly despite there not being an opening that way.