I've had sculpey crack even before baking just from getting old and dry. But with yours it could be possibly a weak armature and slight bending. The baked sculpey is really brittle. Other answer could be if you heated it to quickly which can give you problems with armature/previously baked sculpey expanding at a different rate then new sculpey.
However you should be able to fill cracks with sculpey and bake again. Epoxy putties are good too but it can be difficult to sand evenly since the epoxy putty and the sculpey have different "hardness"
Just curious as to these cracks... is it actually a crack or are the tiny little fractures? If there is a tiny bit of air trapped in your polymer clay when you bake it, you can get really fine cracks in your clay (some call moons). If you use foil in your armature it can trap the air inside (if you don't pack it hard enough) and lead to tiny moons in random areas... it sucks, I know. But even if you don't use foil these little buggars can plague you.
Fortunately there are a couple of cures for this... mineral oil is one (basically baby oil) which you can just apply a daub on the spot and leave it to soak into the baked clay overnight and it'll help it disappear. Some folks don't trust this method and the go in a gouge out the area and basically sloosh around a little liquid sculpey in the cavity and then fill the hole with the regular stuff, then rebake it. I've only had a 50% success rate with this though, sometimes it just makes it worse.
Or course these options for repair are mostly for folks who are trying to keep the "flesh" tone in tact. If you're planning on painting the piece anyway, then yeah epoxy or just straight TLS should do the trick.
IF you are having problems with real cracks in your clay it can mean a couple of things... you might have not completely baked it all the way through, or maybe it's too thick an area, or you can even just crack it yourself if you pull it out of the oven right away and start handling it, because the clay isn't set up yet but still hot and a bit movable.
Anyhow, best of luck in conquering this obstacle, hope you find this info helpful.