Im having trouble where my work files appears to be normal and the machine is confirming everything is homed but in the display it shows my work piece above the CNC area. What would cause this?
In your CAD software, did you define your Z-zero as the machine bed, and then set the Z-zero on the machine to the material surface?
I set my z zero as material surface to both. The odd thing is the first toolpath (3D roughing) went fine its the 2nd toolpath (3D finishing) that this issue popped up
What was the cut depth of your roughing toolpath? The starting depth of your second toolpath should be this depth, so you don’t cut air.
In this example, I want to pocket down to .28 inches. I do a roughing toolpath to .24, then the finishing toolpath down .04 more, starting from .24.
Is it possible that you set your starting depth at a negative value (above the material)?
Sorry. I just realized you’re doing a 3D carving. I better leave this for others who have more experience with that. 
Haha thanks for taking the time! I have deducted that something about the tool changing step is throwing something off. MY machine requests a tool change then that messes up my Z axis. I ran the exact toolpath by itself with no changes and it was fine