Howdy
I have a New Vaquero cylinder in my hand and I can see the 'crescent shaped' marks you are talking about. This New Vaquero has had several thousand rounds through it. I wouldn't worry a bit about the marks, they are so tiny I never noticed them until you mentioned it.
I just checked the parts list of the New Vaquero, and you are correct, the part in question is called the Ejector Alignment Pawl. All it is is a little spring loaded button. Its purpose is to keep the individual chambers lined up to the loading gate. The 'original model' Vaquero lacked this feature, and had an annoying habit of allowing the cylinder to rotate just a tad too far, allowing the hand to pop into the next ratchet tooth, making it impossible to load or unload the chamber unless you went all the way around again. This could get really annoying, and I applaud Ruger for including this feature in the New Vaquero.
What probably happens is, since the edges of the ratchet teeth are basically a knife edge, any slight pressure of the teeth against the little spring plunger causes a slight dent. You probably don't have to slam the cylinder against the button. I wouldn't sweat this at all, the working surface of the ratchet teeth are much larger than the tiny little dents. They are not going to affect anything.