I tested removing all mods except those previously mentioned, and checked all combinations of those three.
Bio Industry is the only mod among them that provides crushed stone and crushers. It provides neither burner variants or a hand-crushing recipe.
Any two of these mods seem to work together fine. Without AAI there is no burner science pack, without Bio Industry the burner science takes regular stone, and of course without SCT the science is vanilla. Only the combination of all three causes a problem.
(It just occurred to me that maybe you think I am using Angel's mods. I'm not)