roughing and finish not linning up

What would cause this problem? Would it be that the roughing and finish tool paths not lining up? The job was built in Vectric x-carve desktop. Zeros where set using OpenBuilds Control probe-plus in the lower left corner.
Roughing used 1/4" end mill, finish used 1/8" ball nose bits.

 

Ok, no probe when swapping bits. So just lower Z until it reads 0 or until it touches the material?

 

Got it, thanks Peter.