List of ores that do not work with 3x3 mining -

Not Enough Roofs mod -
Copper ore.
Slate.

Rustic mod-
Slate

Chisel mod-
Marble
Limestone

Vanilla-
End stone

Quark Marble doesn't work either. Likely many others.

Honestly I would reccommend just implementing it so that any block that can be pickaxe-mined works, by just doing a generic block check and checking if the required harvest tool is a pickaxe and you have the required mining level. I assume it currently uses some sort of whitelist or uses materials or some other strangeness.