Airtable is working as designed. The “allow linking to multiple records” is a user interface setting preference only and this choice is not enforced anywhere else in Airtable.
I’m not saying that I agree with this design choice. I’m saying it is a long established fact.
A common workaround to avoid an item being in multiple boxes is to create a filtered view that only shows items not in boxes. Then in the linked record configuration in the boxes table, limit selection of records to that filtered view.
Note that it will still be possible to create a many-to-many situation by setting linked record values on other ways, such as copy/paste, scripting, and the web API.
As for moving an item from one box to another, that is a different matter. You could group your items by box and drag your items from group to group. Note that this is done from the items table and not the boxes table.
You could use an automation that watches for changes in an item’s box and when an item has two boxes, the automation removes it from the previous box. But automations are slow.
