This is usually due to dust or debris underneath the screen. If you look at the screen closely while it's off, with a flashlight, you should notice something under there. It might be very small.
I've went through a load of N3DS consoles and I will tell you, most have particles underneath the screen. Maybe 1 in 10 have a debris-free screen, and even then, you're dealing with other issues such as a improperly calibrated color temperatures (yellow tint, etc). It's unbelievably shitty QC that Nintendo has going for these panels, nothing more can be said about it
What I suggest is consider how bad it is and consider you might get something worse if you return it:
-Is it visible when viewing straight at the screen? Off-angle visibility isn't as bad as it being visible dead-on
-How big is it? Some are more noticeable than others
-How many are there? I've seen units with 8 or more particles under the screen
-Where is it? The outskirts of the screen is less viewed than the center
-How is the quality of the unit otherwise? Is there anything else that bothers you about it or is it otherwise good?
What's less common is one of the right/left displays has a dead pixel but the other is fine, but this would really be visible at any angle in 3D mode. There are also dead sub-pixels to consider (for instance, a dead red sub-pixel would only look like a dead pixel on red, and would be mostly invisible on other colors since it would simply be the wrong color -- harder to notice).
Many, many things can go wrong. No such thing as perfect, so finding one that's good enough is the key