First off- there are many bugs, it could be.
I never heard of anything being looted in that sense in NMS. When other players invited me, and I accessed their containers, it always showed me my own cargo content, I could not have looted anything if I had wanted to. (A fun way to prevent griefing?)
You can build 10 numbered containers. If you build the same container twice, let’s say cargo 2 on a planet and also on the freighter, it will automagically have the same content. Can you confirm that in your world?
Did you name your containers? I assume names persist. (I recall naming mine, but I started ignoring the names after a while for some reason, so I’m not sure.)
I wonder for example whether you might have moved contents between cargos on the planet, not realising that this would affect a container of the same name on the freighter. (That happened to me once.)
How do you access these cargos? Do you walk up to each and interact with it, or do you use the X menu on the freighter, or from elsewhere?