I'm pretty sure there is no yeast involved here, assuming it's a short crust, and frangipane has no yeast in it. I think the OP said the bubble is forming underneath the crust between the pan and the bottom of the pastry, not in the frangipane itself, so I don't think overwhisking is the problem here either.Im sure we would need the recipe, or at least for the dough/crust. Also what temp are you cooking at? Maybe if you over whisk it there might be too much air? Your yeast or rising agents might play a part in this. I am not too familiar with the dish but I think this is a good starting point and I will let someone else take over from here.
I tend to agree with @flipflopgirl. Although I would be hesitant to dock the pastry before filling it with frangipane for fear the frangi might leak out the bottom. Frangi is a huge leaker. Myself, I would dock and par bake the crust in its pan, let cool a little, remove from pan, fill with frangi and bake the rest of the way.