MoHawk wrote:If the 1/16" end mill slipped there would be a higher area versus being cut to deep.
Steve mentioned bit movement, which could also be the bit moving out. Having once had a handheld router send a bit screaming for the floor (and my foot) because I neglected to tighten the collet enough I can attest to that possibility.
You could try cutting the smaller tool portion of the toolpath first then follow up with the larger area clearance.
Or you could cut with the 1/4" cutter then, if you have space in the pocket for the touch-off plate, set the Z zero to the cut surface. Then manually add 1/8" depth of cut (or measured depth in case it's different) and re-zero through your software. Clear as mud?