There are a lot of "patch materials" suggested here, and they all will work, although automotive spot putty for tiny holes and Bondo for larger ones would be my first choice, but the biggest issue you need to be aware of is; any filler you add, will likely trap air below the material as you try to squeeze into the hole or cavity.
This air will get trapped, and limit the amount of filler you can get in the hole. This is because to mouth of the hole will generally be smaller than the cavity below, and once you cover the opening, the air will keep you from completely filling said hole.
To help avoid this, grind out the upper edges of the hole with an X-Acto knife or a dremel, so that the opening is wider than the original void.
Now when you add your filler of choice, the air has a way to escape, and the filler material will more fully fill the hole. Also, as stated above, before adding the patch material, scar up the inside of the hole (or Bubble as you call it) with the point of the knife or dremel. This will give the filler something to bite into and help keep it from popping out. Now sand and finish the surface.