A lot of staples will have slivers of plywood caught underneath you should either pull out or use needle nose pliers to remove the sliver then hammer then down flush

How to Remove Plywood Underlayment from Laminate Subfloor

Removing plywood Underlayment  can be removed fairly easily. Just cut it into strips as long as there is no laminate backing left. Getting all the staples removed or beat down is by far the hardest part. If it's ran underneath the cabinets use a sharp razor knife and score it several times and it should break off pretty clean.

A lot of staples will have slivers of plywood caught underneath you should either pull out or use needle nose pliers to remove the sliver then hammer then down flush. When you remove the plywood don't want anything sticking up. It's a good idea to refasten the subfloor onto the joist with screws or screw shank underlayment nails. You should see how flat it is too... may have to belt sand some seams.