Sometimes (not too sure about the way re-create the bug though, it randomly happened twice in a row) the bounding box will have the wrong orientation. On the screenshot we can see the hidden blocks are correctly placed but the bounding box itself is rotated. Upon saving and loading, the structure is also in the right position. The problem is purely graphic.
I reached this bug after using load blocks obtained through pick block+NBT (Ctrl+mouse3) then modified to corner blocks; I added a save block from a standard structure-block changed into a save block and got the bug. Note that this chain of event does not always recreate the bug.