The most recent gun out of spec was my custom made 20 gauge fouler. My gunmaker ordered the barrels from the same supplier who had just sent him a barrel that he used to build another fowler for himself. His gun used 20 gauge components, and shot well. our two barrels came in a .626-7 or about 19 gauge, instead of the smaller 20 gauge. He did not even bother to check the bore diameters when he built the guns, because he had no reason to suspect that the barrels would be out of spec. He was more disappointed and shocked at what we found than we were.
We have 3 Springfield Trapdoors in the family, and when we slugged them a number of years ago, we found that Dad's rifle- the oldest-- was a huge, .463" bore. Mine was about .459, the best of the three, and my brother, Peter's gun was about .460. We ordered separate lubrisizer dies for each of the calibers, but found that if we loaded the correct size bullet in dad's gun, the casing could not fit in the chamber, as the chamber was not wide enough to carry the fatter cartridge. Since our father's death 11 years ago, my brother has sent that gun out to Oregon where it had a new steel liner put in the barrel, and the bore is now .458". It also now has 6 lands and grooves, and a faster ROT, being 1:18 vs. 1:22" The faster twist will stabilize longer, heavier bullets. I have not decided whether I am going to have my barrel lined with the new steel liner, or not. I am thinking about it. My brother wants to work with Dad's gun a bit more before deciding to send his rifle off for a liner. You cannot see the seam where the liner and barrel meet. Looking down the barrel shows you the difference.
And, I had a Australian surplus Martini Single Shot rifle chambered for the small .30 caliber cartridge. I read somewhere that the gun would shoot the .32-20 cartridge if the barrel was rechambered. We had that done, but the bullets were all over the map. We slugged the barrel and found out that the bore diameter was way oversized, even for that cartridge, at something about .326" . I was shooting .311 sized bullets, and they were obviously rattling down the barrel. I measured some cast bullets out of the mold and found that if I used pretty pure lead I could cast bullets that would be about .318" Now, that was not nearly close enough, but it was a lot closer to the bore diameter than the .311 bullets. So, I hand lubricated soom of the new cast bullets, and didn't size them, and managed to get them into a .32-20 casing. I began getting five shot groups at 50 yards off the bench that were in the 3-4 inch size, which was respectable considering the poor military open sights, and the still too small bullet. I rebarreled and restocked that gun to .357 Magnum for my father, and inherited it on his death. It will shoot as well as you can hold the sights, iron, or scope, all day long.
I know there have been others that were out of spec, both pistols, rifles and shotguns, but those are the ones that came to mind. Its a lot more common problem than shooters suspect.
My brother's friend is just finishing up repairing a Remington 700 rifle chambered for 7mm-08, a fine cartridge. However, he found that the crown of the muzzle was 3 degrees of square to the bore. Now that he has it fixed, it shoots bullets into one hole, one on top of the other. He also pillar bedded the action, glassed bedded the tang, and recoil lug, otherwise free floated the barrel, cleaned up the trigger pull, and fixed some minor problems with the stock. That is an example of some of the problems that you can find with guns fresh from the factories today.
