MW,
Look and see if the rifling is engraved upon the bullets, which I suspect it has. If that is the case then, besides whatever concerns that you may, or may not, have with the extractor or magazine, you definitely have a problem with either the ammo you're using or there's something wrong with the chamber of the rifle. A key test would be to drop an M-2 spec round (a standard USGI 30.06 ammo would be ideal ) into the chamber, close the bolt and then eject it. If the bullet is pulled from the case, or if the rifling is engraved on the bullet but you do somehow manage to eject the round out as one assembly anyway , then you have problem with the chambering and it's time to see a good gunsmith. The fix could be as simple as a bit of additional "finish" reaming.
If an M-2 spec round can be DIRECTLY chambered and ejected WITHOUT problem then the defect will be found elsewhere, such as the matter of a burr on the backside of the extractor. A weak magazine spring is also a common problem; they simply don't provide enough "push" against the bottom of the round to force it upward and behind a serviceable extractor as the bolt is being moved forward. This results in jams and/or the round otherwise not being in the proper postion to enter the chamber properly, which can cause the dents you're experiencing.
kcw
kcw
As to the issue of mixed parts on your rifle, that's normal as those rifles have been put through at least one rebuild program, or more, by the Army. No effort is made to to use the parts of only one manufacturer at such time. A rifle having all original parts (no replacement parts) is fairly rare.