Is it not simple enough to accept that they didn't show her extracting every single piece?
I really don't see what the big deal is here.

Ill accept the converging shrapnel theory lol.

Claire said because of Luke's cell composition, the shrapnel was moving so all pieces converged in the same area when Claire extracted them.

I mentioned this in another thread, but at one point the gray hoodie he's wearing starts showing blood on the back of his shoulder (as well as the front) - at least I thought it did (though I admit it could have been one of the bullet holes in the sweater from when the beat cops shot at him just before he stole their cruiser). I think it's possible that when it started 'drilling' the bullet that went into his shoulder became a 'through and through' shot. It didn't explode in his shoulder like the bullet in his gut did. It probably exploded underneath him in the garbage truck. So there was no shrapnel in his body from it
Nillindeiel
Agent Hill:
Then aliens invaded New York and were beaten back, by among others, a giant green monster, a costumed hero from the 40's. and a god.
Agent Ward:
I don't think Thor is technically a god.
Hill:
Wellyou haven't been near his arms.
~Agents of SHIELD; Season 1 Episode 1 "Pilot"

As far as I can determine they goofed on the edit.
I had a problem with that especially since the
emphasized
he was shot twice.