The CoGAT is just a screener, so it is possible that he is GT and the test just didn't show it. It's not the gold standard for GT ID, though schools often act as if it is...

I'm also curious about why they didn't look at the individual scores. Many, MANY GT kids are not GT in all areas, and there are 3 on the CoGAT: Verbal, Nonverbal and Quantitative. Many kids show as GT in one but not all. Did they only accept an overall score? Did he break 95% on one of them?
Do they accept outside testing? If they do, you might consider finding a tester skilled in working with GT kids and try a better test.