That surprises me too that staples would be left inside, and I also think that would/cause pain, but then japdip tells us it's not uncommon, and which is also new to me.
My stitches were also closed up with staples and they were rather large, and not something I would like to bear inside. They were on the outside though and all removed. Nothing on the surgical report indicated that staples were put inside.
Apparently, something did get lost inside my body and the 'count' was off. Supposedly, they x-rayed the area but couldn't find anything.
Staples are often used in the tissues beneath the skin and are not removed; this is not a mistake. I would tend to think your discomfort may be more to scar tissue than the staples. You might contact your Surgeon about this but keep in mind that if they were to be removed this would require another surgery. Scar tissue can also be removed if it becomes very troublesome.
I would think that staples would need to be removed. When I had my surgery, the stitches melt away. I would ask your primary doctor to be sure.