Cant place down a oxygen tank shelf or a diving suit locker

What do you mean? Are you using a mod?

I've had difficulty getting the AI crew on and off the submarine when docked to a station, even with both the top hatch doors open. They can't follow me through the connection point.

This is intended as sometimes bots will for no reason exit the ship mid-round and drown. The drawback to this is that bots refuse to enter/exit the sub at stations.

You can ''fix'' this by adding/adjusting a couple of waypoints close to the docking port by using the game's submarine editor.

Hope this helps :)

railgun shoots the ship itself

and now eclipse doesnt work, it blows up the whole thing