I just got 2 boxes of 50ct pine wood plugs. Working on 2x6's (with 2 1/2" screws on 1 1/2" settings), it seems my plug go into the pocket holes deeper than they should, by almost 1/4".
To prevent that, I need to insert a "starter" plug so the actual plug don't end up recessed.
I've searched Google for this issue to no avail. only getting references of the opposite issue (plug not going all the way in), which would not be such an issue for me.
I wouldn't push them in until it "bottoms out"---it's not necessary.
It's intended as a "plug", as the name implies, to close the hole.
Just push the plug in---leave enough material extending above the work piece,
and trim it flush.
BTW---if its hammered all the way down, it'll hit the screw head, and perhaps drive the screw point out the other side.
The pocket hole plugs are designed to be use in material that ranges from 3/4"-11/4" thick. This is the reason that with 1 1/2" material your plugs are sitting below the surface. As Ken described below, you can still use them, you will just need to make sure you do not push them below the surface when gluing them in place. If you have any other questions please let us know.
Use your regular wood glue on all but a little bit of the plug. Use CA glue with accelerator on the last little bit. The CA will set almost instantly as you know helping to keep the plug from going in too deep.