My 1187 will dent 3" hulls when manually unloading as well- No dents when firing. Did a little investigating and the reason is that as the bolt is pulled back manually, the next round from the magazine beats it to the back of the receiver. When the ejecting round hits the ejector button and rotates around the extractor, the rim of the lower shell dents the brass head (and can jam it). The dent is placed at the 6 o'clock position on the ejecting shell, slightly forward of the rim.
This doesn't happen when actually firing because the empty hull is thrown clear before the inertia of the lower shell is overcome and the next shell hits the back of the receiver.
You should be able to manually cycle each round through the shotgun, but you could always pop the two magazine shells out manually under the lifter before removing the chambered round.
You may just need to eject the shells more forcefully. I pull back very briskly on the first round, dump the 2nd round out before chambering it, then cycle the third round.
