Just so you know, these marks on the buttons are completely normal.
I assume they are a by-product of the plastic manufacturing process (Maybe from the machine that removes the plastic from the moulds?)
I have seen these marks on Nintendo buttons for years (Whenever they switched from a gloss to a matt finish on the buttons) My Wii U GamePad and Wii U Pro Controller both have them - heck even my DS Lite had them! The marks vary to some degree, and on some buttons you need to look quite closely under a light source, but I have always seen them.
Ding DIng Ding Ding..... Yes this is in relation as a by-product of the plastic manufacturing process. The first n3dsXL that I got from TRU on Saturday had this not only on the buttons but on the d-pad as well, but the touch screen did not work and there was a gash on the left side of the top screen.
The second one that I have now, from a TRU closer to home, is perfect.... I do have the same plastic markings on the buttons and d-pad, as well as when the light hits it just right on the interior plastic of the system (black n3dsXL) here and there, but is not as bad and you have to shine it like 99.999999999 just right to see it.
The hinge is better, it barely moves compared to the first one, and both screens are flawless. Not to mention the buttons are tight and responsive. It is just like my earlier post the only concern was that the c-stick is about a hair off to the right than completely centered. I so did not want to return this one again, and tried to "massage it" back to center.
Well after work today I went by a gamestop looking for a Megaman amiibo, and lo and behold they had their display n3dsXL with the same thing but to the left. After moving it a bit (both gently and really really hard.... then wiggle) it went back into place. Started the game up and used the camera in Majora's Mask and not only was it working perfectly but it was centered. I just got home and continued to gently nudge it and viola... it is now centered.
Sorry for my long rant..... I had to get this out of my system..... I just did not want to give up my n3dsXL and risk getting one worse than what I have. I am sure many others on here would agree with me on this.