I would wash it in hot water and soap. If regular hand soap doesn't work I would try something stonger like Dawn. If that didn't work I would put it in the dishwasher. If that didn't work I would send it back! I know the box it comes in is black, but that shouldn't stain the toy! If I couldn't get mine clean I would send it back. I hope you like your Ella, I love mine!
I'd try a few different things first; various soaps, various methods of cleaning, try everything first... then if you still have marks on it... what do you want to do? Have a perfect white Ella? Then send it back. If you like the character of the marks, keep it.