[The Stiff]

I am a coach looking for some guidance on calling obstruction. Situation was: I had runner on second with two outs. Bloop single to center field. Shortstop is in the baseline, and my runner and the shorstop do the hokey pokey before my runner gets past. I see the umpire put his fist out, so I waive my runner home figuring that, if she is out, the call won't stand because of the obstruction call. She was in fact out, and the out stood as I was told that the obstruction call only got her to the next base (which at the time was third). Is that the correct call?

Seems odd to me since she would have easily scored had the shortstop not obstructed her. If that is the correct call, why not have your shortstop do that on all base hits?

Thanks in advance for any interpretations here.