Yes that's right: if the IDs are not being scanned properly it is most likely due to lighting. Mobile scanning is not like scanning in a machine. Glare from light above can reflect off of the pencil mark and make it appear silver or white, and the scanner will have trouble recognizing it.
It's easy to see whether a bubble will be recognized by the scanner during scanning. Just look at the bubble sheet through the viewfinder (the screen) and see whether the bubbles appear to be black or grey/silver/white. If they don't appear black, the scanner won't see them.
Usually, all it takes is moving away from overhead light, or moving your body or the sheet so that light from above is not glaring down directly on the sheet.
For most people, it takes 5 successful scans before they have no trouble getting 100% accuracy, all the time. So please just practice a little more, look at what the answer sheet looks like on the screen while you are scanning, make sure every mark appears black, and you'll be good to go!
And if you still have trouble, please submit a support ticket through the support tab in the mobile app or web app, and request a live scanning tutorial. We will help you out!