Rough/bur edges on the Carrier U slot is kind of normal, and just take a file to smooth then out. Hence with the U slot edges smoothed out, will not be marking the face of the buffer.
As for the dent in the U slot, really need to see how much of the end of the receiver extension is holding the buffer retainer in place. Hence with buffer receiver threaded in to retain the buffer retainer pin, edge of the tube should be lightly kissing the center pin of the retainer.
If the buffer retainer with spring is installed correctly, and the receiver extension lip is over the back half of it to hold it in place, but the face of the buffer is making contact with the pin to start to bend it when the upper receiver is locked home, then buffer retainer pin channel as not drilled in the correct location. Hence back of carrier should be pushing the buffer off the retainer pin as you close the upper receiver. So if buffer pin channel as drilled too far rearward in the receiver, either need to have the receiver replaced, or swap out to a off set buffer retainer that has it pin a touch more forward instead (allows the buffer to be held in a little forward, and when the upper is closed, back of carrier will push the buffer back off the pin instead.
As for gas key and even the gas tube, the gas tube should be centered on the gas key and free floating in both upper barrel nut channel/spine, and upper receiver gas tube channel. Hence gas key centers in the charging handle channel, and gas tube centers in the carrier key (no way for the key to make contact to the upper. Now having said all this, take a good look at the back edge of the barrel extension, and it should every so slightly protrude back into the upper receiver void, past the front wall.
As for back of key, real easy to check if you have the correct parts in play, and just pull all the way back on the charging handle, and the front of the bolt should stop 1/4"~1/8" in front of the back edge of the charging port. Hence too short of a buffer for the stock set in play will end up with the bolt retracting back too far, and chancing it making contact with the lower receiver thread ring (to crack in on an impact). Also, if you have the correct recoil spring it play, should be able to pull the buffer to put it face down on a bench, then compress the spring all the way down until it coil binds out. Once it does coil bind out against itself, top of the spring should be below the top of the buffer bumper.
As for charging handle U slot, carrier key snout should not be making contact with it. If it is, either charging handle U slot and channels are out of spec, or the key isntead.
Simply, if this is a factory built rig, then send up back to be repaired. If a kit you put together, then get the supplier on the phone for replacement parts that are in spec isntead.