»Lol, now this is a flaw that NOBODY CAN DENY«

Remember in M3 everyone who was abosbed by smith goes back to themselves so some of their code is still there. Also listen to what smith says to Neo when he sees him after Neo's meeting with the Oracle. Part of Neo was copied or imprinted onto smith. Smiths code had to have looked different after absorbing someone combined with some of Neos code. Also Smith wasn't an agent in M2 or M3.

Cypher tells Neo that he doesn't even see the code anymore, all he sees is blondes, brunettes and red-heads. Morpheus looked at the code and saw Smith. Link, an operator, made some additional observations the same way any specialist observing a phenomena would compared to a non-specialist.