Plywood repair - subfloor prepartion - subfloor leveling
Cut out the missing sections to match pre cut patches that span joist to joist.

Assuming 16" centers patching a 10"x10" hole.


Cut a piece of 5/8 ply 16x10
Place it over the hole covering half of each joist and fully covering the hole.
Pencil your impression.
Set saw depth to a "light" 5/8" and carefully plunge cut the lines, remove any screws or nails first. A magnet helps to find them if they are buried or filled with debris. (I always pass a magnet over for cuts like this)
Use a prybar to pop up the section and chisel anything else in the way.You can also scab in a scrap along the underside of the floor under lapping the patch.
Glue and screw your repair peice in.


Edit

It's not a ton of work but I do understand your question better now. It would be a bit much to correct just a single lamination from the ply missing. You can simply use a putty type of wood filler. Or anything to prevent the laminate from dipping. I've seen guys use construction adhesive like PL to repair small defects in the subfloor. It's messy and doesn't spread very well, but if they are using a tube elsewhere they often try to use it up as it's a pain to reopen for additional uses.

Second edit

The picture shown probably wouldn't need to be repaired but it doesn't hurt to fill it.