I've been having the same issue, particularly with trying to place units on the side of a hummingbird (also happens with the other helicopters too). In the editor it will look fine but when testing the mission the player will be placed in the copilot seat, with the original copilot unit being placed on the side. When going back to the editor, you see this as well.

You can replicate this just by spawning a helicopter (with the ai units), then dragging the player into it and running the mission.

A temporary fix I found is to group the player with the helicopter. You can even ungroup the player straight after and he will still be in the correct seat.