You probably have to look closer at the ones that do not
copy (or maybe they just do not select? Are they at the
current level?).
I've used the same scheme, copying all of the top level
pad pins to another 0,0 layout for blowback re-LVS.
And my layout style always has pins on pads in I/O
cells, which look just the same from the top view, but
those pins are not selectable at that level. Maybe this
is what's going on - the pins you think you see, are
really part of some subcell.