The valves should spin as the motor runs, sounds like you had a couple that were not turning correctly or bent a little?, and got hammered. They can leave little chip marks or work one side of the valve stem as you have probably seen.
That is pretty sneaky what those machine shops put on the heads to service their warranty, lol.
If your changing the oil with the new head (which you should) be sure and fill the new oil filter up with new oil too, until all the bubbles stop coming to the top. It will give oil flow a little head start to the head. Some people even will pump oil into the rocker rods for the initial start. Just take your time and you'll do fine. Re-torque after a few hundred miles and it should last a long time.