Could be a factory plug to eliminate a small blemish.  New Misfit Pearl from where?

It should have been marked as a 2nd if you ask me.

It wasn't perhaps sitting on the towel in the box outside the bag was it?  Or was the towel resting on top of it on that spot?  I had one of those, and I use the microfiber towels underneath my bowling balls in the bag to cushion them and because sometimes dirt or debris or something gets in the plastic cups in the ball bags and can scratch the ball surface.  HOWEVER, with the yellow Misfit, I had it sitting on a black towel, and it started "bleeding" onto the ball, or it started absorbing the color and that put a similar looking darker spot on the ball.  Even the gray towel "bled" some color onto it. 

I'd keep it.  You may have the only one in the world like it.  There was probably a tiny bit of green left in the color tube as it was mixed. 

I have also seen the dye from their microfiber towels bleed into the covers of the Misfits by them sitting on the ball (inside a locker at room temp).  In both the gray and black towels it bled black into the ball.  (A gray towel is probably black and white dyes mixed)

I tried resurfacing, etc, but it got into the ball deeper than the small amount I resurfaced off.  It didn't affect the ball's performance at all, just a color thing.

Misinterpreted what was meant by "dark  spot"...  I'd have drilled it, but I gave my Misfit Pearl away...  Just not the right ball/layout combo for my game most of the time so the novelty wore off rather fast.

I looked at mine and it has a similar spot on it. I also looked at one of our high school bowlers that I coach and his has a similar spot. I don't see a problem with it and I think notclay is correct with color mix!