"The Bug" and the agents as a whole make no sense
"You are going to help us, Mr. Anderson - whether you want to, or not." also makes no sense.
What did the bug do, exactly? Such a 'nightmarish horror scene' when it was inserted, all that flailing around and shutting Neo's mouth - and for what?
Seriously, what did 'the bug' actually do? It was inside Neo's (virtual) body for a LONG time, and it did.. what, exactly? Move around a bit, disturbing his (virtual) organs? Created internal bleeding? Brainwashed Neo a bit? Installed 'proper values'? Made Neo a machine spy? Inserted a long-lasting drug that makes him susceptible (not sure of the spelling here) to the Agents' control?
What is the point of installing something into someone's body that does ABSOLUTELY NOTHING and is then promptly removed? Was the plan that it was GOING to do something... not now, that it could, because it's inside Neo's body, but some time in the future, when things are happening? What? Huh? How?
It's one of the most dramatic, surprising, intense moments in this whole movie and the story, and yet it's 100% useless. The agents might JUST AS WELL not even have come to Neo's workplace, the end result would be the same!
If you want to argue, please explain how it would be ANY different. Neo would still have probably taken a nap, Morpheus would still have called, etc. etc.. EVERY DARN THING would still have played out the same, so as a group of agents, why even bother showing up, when you could have just spent the day off, like Ferris?
Furthermore, now Neo knows something is wrong with reality, and his determination is going to be even stronger. Why show anyone these 'reality-breaking things' if you don't have to? If they were gonna control Neo anyway (mouth shut), then why not control his MIND instead of his body? Just make him fall asleep, then insert the bug, so he doesn't know about it. Why not this way? If they can shut his mouth, surely they can shut his mind as well - or heck, even just his eyes would be enough.
If they're gonna inject something into his body against his will, why not a sedative or tranquilizer first, at least? THEN do your 'reality-breaking stuff' when he is asleep. Why give him this info and then let him think it MIGHT have been a dream, when you absolutely did NOT have to reveal anything at all?
WHY are the agents so SLOPPY when it comes to this 'revealing things to people' stuff? even MiB were better at hiding things from the masses. What about the cop that says 'That's impossible!'
What kind of existential crisis is he going home with? What about all the people, whose lives they just interrupted permanently by taking over their bodies? Shouldn't there be some kind of protocol for this stuff, so they don't just indiscriminately disrupt people's lives in a way that creates a butterfly effect that eventually makes the public realize the truth? What if people start investigating why someone suddenly disappeared, etc..?
The agents make such rash, stupid decisions, it boggles the mind.
Then the whole mouth-shutting thing - what was that? How did they do that? Why did they do that? What was the point of it? Was it necessary? I don't think it was, and yet, they just FLEXED on someone just to break the illusion of reality - again.
Why do they keep doing this without a care on how it affects the CAREFULLY crafted 'worldbuilding' and illusion? With this kind of carelessness, it won't be long until EVERYONE knows what's going on!
They don't seem to be worried at this stuff at all.
I mean, they could easily take the body of some mother, whose kids are waiting for her at home, and the mom never arrives. So now what? Do the kids starve to death? How can they just keep doing this stuff so easily and sloppily?
Furthermore, if they are SO willing to so easily disregard any discretion, why won't they just simply do MORE of that 'reality-breaking' stuff, like jump from rooftop to rooftop instead of using a car to travel, or use cops to help them? They could do this job all by themselves.
Also, why would the agents that can BEND REALITY, need some corporate secretary telling them WHERE Neo's cubicle is?? Come on! How can they be so 'omnipotent' and yet so ignorant at the same time? Their 'running search' was not very extensive, if they have to talk to some low-paid plugged-in battery just to get directions to Neo's cubicle.
I mean, think about it - would you lower yourself to TALK TO YOUR BATTERIES if you had a much better way of knowing something? WHY would the machines and their 'sentient programs' (groan) NOT know every single thing there is to know about The Matrix? THEY ARE RUNNING IT! THEY CREATED IT! THEY DECIDED EVERYTHING ABOUT IT!
They should basically EVEN know everyone's thoughts, for crying out loud. But they can't find Neo's cubicle without a battery pointing it out? WHAT?!
That's like you not being able to use search engines to find some address, so you have to ask your Laptop's battery for directions. That should NOT be how anything works!