Due do the attempted fix for
MC-1973, a single item is now dropped out the inventory slot of beacons when closing the GUI (if there is any item inside).
Apart from the fact that items can still stack in beacons (using hoppers or 1-9 hotkeys) this behavior has another negative aspect to it: Malicious players can repeatedly open and close a beacon's GUI to prevent players from setting an effect on it; this is because every time the inventory is closed the item inside is dropped, even if someone else placed the item.
I suggest undoing the attempted fix for
MC-1973 and saving items in the beacon inventory slot instead. This would fix this issue, MC-1973 and MC-7222. Or maybe it just shouldn't be a storage slot, but rather an item slot like on enchantment tables or on anvils. Either way, it's a bug.