When the bounty hunter shrinks Aeryn, her cuffs are gone. But when she is inside the canister Chrichton takes from the dead bounty hunter, she is fastened to the wall of it by the magnetic cuffs she was wearing before she shrank.
When the crew are shrunk and in containers they are shaken and jostled. this would cause head trauma.
Before being shrunk chiana and shanu are with pilot. aeryn and rygel are on the bridge. when they are in the canisters chiana is with aeryn and rygel is with shanu.