Assuming that Eleven ordered the fez, one can forgive Kerb!am for the late delivery when they remember that the Doctor and the TARDIS don't exactly sit in one spot (or time) and wait for delivery.
The reason the Kerb!am system tried to assign the Doctor to maintenance was so that she would be led directly to Charlie.
Why didn't the Doctor's package have explosive bubble wrap? Because Charlie's plan was for all of the explosive packages to be sent at once. As a result, all of the packages with deadly bubble wrap were being held in delivery while packages with normal bubble wrap were being sent off, because it would be very suspicious if all of Kerb!am's deliveries were suddenly late. Despite Ryan's worries in the last scene, the bubble wrap in the Doctor's package is perfectly safe. If not, the system itself probably made sure that its cry for help wouldn't blow up the message's recipient. Heck, it may even have looked up the Doctor and discovered that the Time Lord's long-ago fez order offered it the perfect chance to summon up assistance!
The callous nature of the way the system killed Kira makes the Doctor's claim that it has a conscience a bit jarring, but it does kind of make sense. The system's main view of the world is the warehouse it oversees, and it sees that Kerb!am's workers are dehumanised and treated like interchangeable resources. Kira is an employee, therefore it can get her hopes up that she's Employee of the Day and give her an empty present that's actually a death-trap with an entirely clear conscience. It means well, but just doesn't know any better. In addition, the system probably used cold mathematics to calculate that killing Kira would be an acceptable loss and preferable to allowing Charlie to murder millions of unsuspecting innocents . It may have a conscience, but it's still a computer at the end of the day.
This episode its somewhat reminiscent of Asimov's last story in I, Robot, in which five robots in charge of overseeing the workforce (one in each territory) all simultaneously started acting odd and violated the first law in the process by harming individual humans. The story basically went through a similar premise: in each of the territories, there were humans who ended up high in the food chain that wanted robots gone. Because humanity as a whole were better off with the robots than without them, the robots in charge of the workforce were able to circumvent the laws by pulling a The Needs of the Many. It could be that this story is an allusion to that story, or a accidental inspiration, either way would hint at the willingness (on the robots' part at least) to let a few people die (or actively kill a few people) to make things better for everyone.
It's possible that the system was aware that killing Kira was evil and wrong. But it tried to avoid doing it, and instead used every other method it could think of to stop Charlie before finally resorting to murder. It's not unlike the Star Trek episode "Thine Own Self", where Deanna is in a holodeck simulation of an emergency as a test. The solution involves sending someone on a suicide mission to fix the problem. However, the secret test is making sure that the person being tested will use the "suicide mission" option only as a last resort, and will try every non-lethal possibility first.
If Charlie's plan had gone through, consider that the first object that the Doctor opened was a toy. The bubble wrap was around a toy. And who in the household is typically the first to start popping the bubble wrap? The victims would have almost certainly and overwhelmingly been children. And was that something Charlie considered when he determined to ruin the automated system, that a majority of child victims might have incurred an even higher wrath from the public?
