For a guy with IQ 300, he should've noticed.
Or probably he is but he just don't really care.
Smart people tend to be oblivious to the immediate things around them given their brains are on a higher level. Plus intelligence doesn't excuse personality given Dr. Robotnik was a self-centered person in the film.
Plus, it's only a guess of mine that Agent Stone harbours affection for Dr. Robotnik. If he does then even we didn't know ourselves from the first movie.