The school is simply saying that your son needs to be seen by an eye doctor. He did not pass the test at school, but the test at school is just a screening. It's a way for schools to identify kids who probably need to see an eye doctor. It is not a thorough as a eye exam from an optometrist or ophthalmologist. It's just a really good way to catch kids you might benefit from an eye exam.
In Illinois, all kids must see an eye doctor for an eye exam (vision and eye health) before they can begin kindergarten. So both of my kids have been to the eye doctor.
Our doctor said that at that age, it is totally normal for their vision to be a little off, as their eyes are still developing. With both of my boys, he said their vision was not 20/20. He did not, however, recommend glasses at that age for 20/40 vision (which, by the way, is all that is required to get a drivers license ... 20/40 or better in both eyes) at that age. My oldest did later need glasses, but not until 2nd grade.
My guess (and it is a guess) would be that that scratch could interfere. I'm not sure why it would "worry" you. The school is just letting you know that your son might benefit from seeing an eye doctor. Your son is already under the care of an eye doctor, so there's really no reason for you to worry. If the eye doctor didn't already check your son's vision, make an appointment for that. But otherwise, no worries!