Z-Axis cuttting to deep and cut not completing

Alright so I’ve tried my X carve again and I ran into a problem all was well at the beginning so I let it go. When I came back at the end I saw this obviously something is wrong with the X-Carve but I have not been able to identify it. Also my nut on my M8 threaded rod is rattling down the shaft to rest on the spindle mount is this ok?

For reference I was trying to cut this https://www.inventables.com/projects/les-paul-pick-holder.