I am trying to cut a simple square out of my stock.  My stock is .75" thick.  My G Code sets the Z to plunge and cut to Z-0.75.  The Axis begins to plunge about half way, then appears to do a small bounce upward, then cuts leaving a cut depth of about -0.25.  Once it finishes the square cut it begins to cut air on any other geometry that is after the Z-0.75 cut.

Can anyone help with this?

Put the code up so we can see what it's doing,  also if you need .75 and your code says .75 you will need to add for clearance over the material, so make you commanded depth .8 or so.