New? theory about machines destroyed at the end not MIM

Agent smith tried to turn neo into another smith and wasnt able to completely copy himself, but possibly bits and pieces of smith remained on neo's code allowing him to control the sentinels like smith can
the same could have happened in the reverse when neo bonded with smith

neo set smith free
smith tried to enslave neo

When Neo jumped in Smith in M1 he freed Smith from being an Agent and thats why he can copy himself.(Neo was too powerful to clone).