Can't see your pic here at work, but I think I understand what happened. I've only used a Campy extractor, which does have an end piece on the extractor bolt, but it fits inside of the arm taper quite easily.

Are these NR/SR cranks? The spindle should not be flush with the inside flat surface of the crank arm, but should be below it. IIRC, Kurt had posted a pic in another thread showing what one should look like.

As for your crank arm? Not sure; if it were me I would put it on and see what happened. I would think the spindle should push it out a bit and back into its original shape somewhat? I would probably install it, and then remove the bolt and take a look to see if any aluminum was sticking up, etc.