Since they were buried the containers themselves couldn't be seen on the ocean/lake bottom and it was quite hard to exactly line up the purple blips to get the message saying what was in them but it could be done, however what happened is this...
The terrain walker cargo space started filling with water while the ship's cargo space started loading the contents of the buried container at the same time (I only really noticed this as I was also running EM Tool on a second monitor).
Also the sound would indicate that the container (fusion) was loading while the cargo of the TW had filled to capacity with water (since the TW walker mines quicker than the ship), and I wasn't getting messages saying no room for cargo type water. I moved on to another container with missiles and same thing happened, got messages this time saying missiles were full but they started filling the ship's empty cargo spaces, as per normal when doing it in a ship, and the same for a cannon in a third container (i.e. standard message you would expect for tractoring from the ship).
Not sure if this happens with all permanent containers (i.e. purple blip types) and the TW, but I suspect it does, as In my experience, mostly these containers are either buried to an extent they are inaccessible by both ship and TW, or are floating above the planet surface or in space, and need the ship to tractor them in, one exception I can think of is the Missiles in the ship wreck on Olympus Sigma we're told about as part of the IMG Quest, in that this one I presume is reachable by both ship & TW (I usually just grab it by ship for the reason: I figured I'd have to do numerous trips to get more than one missile with a TW... something that may not be true as they would possibly get beamed straight the ship)
Anyway I just wanted to post this as info of a possible issue for those that have single monitors or don't run EM Tool as without knowing about it you would mistakenly think you were picking up something else (i.e. some mineral) and not the containers contents when in fact you were doing both, only you wouldn't realise until you returned to your ship and checked the cargo screen.
I'm also not really sure if this is a bug or by design as I for one can definitely see the appeal in having things like missiles load directly to the ship rather than have to make multiple trips to load up on missiles with a TW should the container be unreachable by ship (as was the case with the containers I found on the undisclosed uncharted planet I noticed it on - and seems to be a pretty rare situation)
I guess that last paragraph is me saying it's probably a bug but I like it so prefer to think of it as a feature




