Same issue here (PC). Basically the Freighter base building is made up of square cells. Depending on the selected part to build, existing cells next to it, should adjust to connect properly. They just forgot to add this to the Storage Containers. Building cells used to be the same size as cuboids and thus the same size for Storage Containers, but this size has somewhat increased. So without having added connecting functionality to the storage, you end up with empty gaps. As a side effect, there is no collision either, great! I also assume this is not dependent on the floor, likely having the same result a floor up, although not tested.
I think I’ll either restrict use to my planetary base, or go with @kpd157’s solution.
Note: Content functionality is basically still the same. You can build any of the containers in any of your bases, keeping it’s content. This means that now we can build bases anywhere, it would only cost 40 Chromatic Metal (Base Computer) to have access to storage container content ANYWHERE you need it! Not yet sure how useful this may be, but it is an option 
Images
Yep. I have 10 on ground & 10 in my freighter. Can send to them anytime but sellective storage means direct access. So far very useful.
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Sorry to necro an older topic but it’s the logical location since it’s the only relevant topic I could find.
(@temp I altered the topic title slightly to suit)
PS4 NORMAL LEGACY SAVE.
Problem: On my S freighter, I had 2 Frigate Control rooms either side of the corridor that leads to the bridge.
During my recent renovations, I deleted these 2 rooms without deleting the couple of decorative parts inside. Instead of automatically deleting these decorative parts, they now remain in place preventing placement of an alternative room piece in that location due to collision.
This has ruined these build points & I’m not sure how to correct this.
Let this be a warning to others…
Question a): Is it possible to delete a freighter’s internals or does this only occur when swapping freighters?
Question b): If I were to swap freighters, can I immediately re-buy my old freighter & will it retain the S class rating & size?
Question c): When a freighter is swapped without manually deleting, do ALL the build materials get recycled or do you lose some, (like old Atlas Rises bases did)?
My frighter is substantially built out so there is a lot to lose if it doesn’t recycle, plus there is the issue of the Base Salvage Capsule dumping 2000 of whatever into your suit inventory everytime you get something out.
Thank you you fellow travellers in you assistance with fixing my Legacy game freighter problem.
Edited for clarity.
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I ran into this issue once, quite some time ago. I was cleaning up my freighter to create a new design. I usually work inside-out when deleting, just to make sure I don’t lose anything. Instead of removing a small refiner, I accidentally clicked the room. I then had the same issue you described, no longer being able to place the room back, as the refiner was actually still there and now blocking placement.
I did get lucky though, as I was able to place a corridor instead, which got me close enough to reach the refiner, even though still behind the wall. I could get the interaction to show up and remove it. In other cases you may not be so lucky, even more so if interaction is not an option to remove said item. In your case decorative items, which require line of sight to be removed. This basically means it will never be possible to remove, as the only way to make part of it visible again, is going to result in collision.
The only way to possibly fix it, is by somehow managing to glitch into the interior of your freighter to then reach the item(s) for removal?
To answer your questions:
a) There is no ‘reset’ or ‘delete all’ option. Only on PC could you make changes through a save editor.
b) I don’t believe you can re-buy your freighter right after purchase of another one. As soon as you buy another freighter, your previous owned freighter is gone.
c) I believe the Salvage Capsule only works on planetary bases. On freighters you used to just lose everything. I haven’t tried for a while, but I honestly think this is still bugged. You could give it a try of course if you have a backup to work with.
I feel your pain … good luck!
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This reminds me of a vid by @kyle-culver where he showed a way to glitch through the Freighter walls by aiming for the central lights in the hangar. I did it once and could see through walls. It was a bit scary though as I was not sure I would be able to get back inside but it worked out.
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Perhaps I should just live with it the way it is. 
Thanks guys.
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