Presuming you are not on a server with regenerating POIs, you can add a salvage core to the shipyard and use the F4 menu to see check all of the (non-alien containers) to see if there are any you missed.

Salvage each container you loot along the way if you can, it will make identifying any missed a lot easier. Also, if you salvage all the cargo containers do the devices lists them at 0 and then check the CPU statistics, if there are any cargo containers remaining in that list it means there are alien containers you did miss (quantum containers should still be listed in the F4 menu if they exist though).

Thank you for your reply. In my experience quantum containers are not listed in the F4 menu. I never thought to check the CPU statistics, I will do that. Thank You :)

Edit: I took out all of the containers listed in the p menu and one cargo container is still listed in the statistics. So far I have spent another hour looking for this one container.

Edit. Ok so I finally give up. The only reason I invaded the Zirax Naval Shipyard was for the quantum chest. But since they made it so damn hard to find I will never invade another. Nobody should have to spend 4 hours searching with no success.

Edit: I didn't realize until now that statistics counts closets as cargo containers. The quantum containers are also not listed in statistics.