I think the confuse here is what is the map of? Is it our ship we are on, or the cargo ship we are trying to dock with?
the ship you are docking with, the ship you took was just a small shuttle.
Keeping with my "heavily modded' theme, I'm going to suggest that we're actually in the carrier pod of a cyborg space yetti. This particular space yetti can shoot iron javelins from its eyes.
I gotcha, lets go with the top level with the bridge and engine room.