That was what I thought of. Ax is young, and may have never seen Alloran personally. He's just a cadet, so maybe they didn't feel the need to tell him V3 was on the planet, and what his host looks like. So it could possibly work, and shows V3 has cunning.
Then he goes and tries to hack down a door by striking it in the center instead of around the knob or hinges, then morphs Human before running through the doorway to face the Andalites. All those clever points gone down the crapper.