You have to pre-compose the tracking to neutralize the coordinates and/ or the pther way around - apply the puppet before tracking the layer in teh parent comp. Simply limitations in how distortion effects and in particular Puppet work.
I did as you stated, but when I whip pick the Puppet Pins to the face tracker points the Puppet pins all go to one spot. The position numbers are exactly the same yet they are not connecting. Please help
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If you pick whip the position of a null object or a small solid to the tracking points, do they follow it correctly?
If so, you just need to use some form of the toComp feature in the puppet pins expressions or precompose the mask layer (moving all attributes) and apply the puppet pins to the precomp.
Here's the thing, puppet pins' positions are relative to the layer itself. The face tracking data is the same. However, your two layers are likely very different sizes so the same position value on the main layer isn't going to be "the same" on the mask layer. So you need to make the coordinates the same. Thus the two options I gave (precomposing being the easiest).