The Matrix 1.0, the heavenly one was not disrupted by an anomaly. Rather it was destroyed by a cataclysmic system crash, since no human there would accept it.
Matrix 2.0 (the one we’ve seen), is running now for the 6th time. Morpheus only knows about this 6th run of Matrix 2.0, and the MAN he refers to, was the fifth anomaly, who was allowed to take 23 men and women from the Matrix 2.0 run 5 and rebuild Zion.
We know nothing about the FIRST One, the anomaly in Matrix 2.0 run 1. He may have been freed by free humans, since there is no reason to believe the machines caught all humans at the end of the man-machine war. Not freed the way Neo was, with people hacking into the Matrix (the free humans at that point would have no plugs, unless they fitted themselves with them), but either he freed himself like the kid and was fortunate enough to be found, or the free humans raided the “batteries”. Or the machines, knowing about the paradox of Matrix 2.0 helped free the first human.
The Architect who wrote Matrix version 1.0 and 2.0 would have expected the anomaly. He says in M2, that there was an inherent paradox in giving the sleeping humans a free coice.