You are always going to have some breakout of the surface veneer of
pretty much any plywood when you try to jam a punch through it, which
is what is essentially what you are doing (I'm assuming from your post
that you are using a square chisel mortise attachment or mortiser.

If you wanted, you could use a very sharp razor knofe and score/cut the
surface first. Yes, that is a bit manual intensive, requires layout
that a mortiser typicially helps you avoid, but if you want clean cuts
in plywood, I couldn't see any other way top get it.

BW