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