The scanner has to do a balancing act: it should not pick up marks that are very light because those are probably erased marks that should not be picked up. But it also should recognize dark-enough marks that were intentional. Having to ignore marks that were erased (but not completely, since no erasing is ever totally complete), but also pick up marks that might have a little light bouncing off of them is a tough job.
The solution is actually pretty easy to achieve: don't scan in an area with strong overhead lighting, and make sure when you look at your bubble sheet on your device's screen, all the marks appear dark in color.
Take a look at this bubble sheet to see what happens when too much light is being used while scanning. You can see that the whole last column of bubbles appears silver in color. The scanner will interpret these as erased marks.