Hi, MissRhosie,
Don't know if your soap cutter is the problem or not, but Honey is right, forgetting to spritz with rubbing alcohol between layers and hurrying the hardening along by sticking the soap in the fridge could cause the layers to separate.
Something else that popped into my mind was that waiting too long between layer pours could also be the problem. You want to pour the next layer (make sure it's not too hot!) when the previous layer of soap is still warm, but has a thick enough skin to support a new layer. This usually takes about 20-30 minutes, give or take a few depending on how thick your layers are. Check to see if the layer is hard enough by blowing on it gently. If you see ripples, it's not hardened enough.
Don't know if any of this applies to you, but these things can cause layer separation.
