As an M16 / AR15 armorer I have to chime in on this one. First off the marks and scratches on the bullet itself probably will not effect accuracy to a noticable degree. I have personaly fired rounds where the lead tip of the SP ammo was badly deformed and the copper was noticably scratched but it went to POA like the rest.
As far as the rifle goes. Single loading one round at a time or loading a round then inserting the magazine SHOULDN'T effect the function of the rifle. There are however many other factors that COULD contribute to a malfunction of a rifle loaded in this manner. The biggest factor is DO NOT insert a fully loaded magazine of any capacity under a bolt closed on a manually inserted round. Always under load your magazine at least one round I practice and teach down loading 2 rounds, ie 18 in a 20 or 28 in a 30. My personal 5 round hunting magazines from Bushmaster will not function if there are 5 rounds in them. So...I load the mag with 4 and load one in the chamber by hand for hunting.
An AR shooter will have more function problems due to bad magazines, weak ammo short stroking, loose gas key or other gas system issues than from loading a single round by hand.
Lastly inspect the unfired round ejected from the chamber before loading it a subsequent time to ensure that the bullet was not pushed deeper into the case as this condition COULD result in a pressure increase and cause some other problems.
YMMV.
