I think we're going to need a clearer explanation, or better yet, a picture.

Are you saying the threaded end of a crank puller won't thread into your crank arm? If so, have you removed the bolt or nut first? That has to be removed before your puller will thread in.

There have been multiple crank puller sizes, but there's only one standard today (22 mm). The others are long obsolete and were specific to particular brands like TA (23 mm) and Stronglight (23.35 mm). The current standard is the smallest of them, so you won't find a smaller one.

The plunger on a crank puller, or the piece that pushes against the end of the spindle, does come in multiple sizes however. You'll want the smaller one, for square taper cranks. The plunger for splined cranks like ISIS or Octalink is a bit larger. Some tools are capable of both, either with a small adapter or via a reversible plunger. (The Park Tool CWP-7 is one such tool with a reversible plunger.)