»I just realized. The humans are still screwed.«

The song called wake up starts to play as soon as neo bangs the phone down..
This phone put down cannot be a wake up call to the machines... The lyrics are about people waking up to the system{ Knowing truth}

the machines system gives them the warning with the carrier anomaly warning...

The machines cannot know that neo is an anomaly.. It is the machines system that warns them remember..

Neo felt the machines and knew that they were scared....

Funnily enough the trainman didnt seem to scared of neo did he...

Neo has complete mastery over the matrix....

The matrix is linked to the machine world.
The agents are the firewall
Neo can destroy agents...

The code in the message stops falling and comes to a halt..This is where it says SYSTEM FAILURE..

Neo obviously got into there systems and corrupted them...

Neo could do as he liked....