You really need to pay more action when watching shows. Claire mentioned after studying Luke's tissue sample that the shrapnel pieces are moving so they were converged into the same area when Claire extracted them.

My wonderonce was why did they need to immerse him in acid, when wouldn't simply covering the area around the wound be enough ? His legs were dunked but there was no wound there, his arms too, and his head, and his back and his junk. All these parts had no wounds, so why was it necessary, other than for ae visual purpose. Maybe a cut scene has him ask this very question afterwards and she gives him a Doh! expression along with a my-bad.

It was the gut wound extraction only. Thought the exact same thing. Did I miss something when they showed only the gut and not the shoulder shrug

Go watch it again. It is definitely the gut wound.

Which is why I added the "Either way." part.

No, they worked on the shoulder more. Barely even saw them go near the gut wound, if at all.
Maybe it was supposed to be implied that they did it after the shoulder.
Para tiempo means nada nunca.

I actually saw the exact opposite - I thought they only went after the gut shrapnel and ignored the shoulder. Either way, the filmmakers were definitely sloppy with the consistency in that scene. He had two wounds and should have had two separate shrapnel-extraction sequences.
I'm guessing they were just trying to play up the suspense and drama of barely getting the last piece of shrapnel out before he flat-lined again. Trying to go after even more shrapnel under those conditions would - for the viewer, at least - have been overkill.