In the movie Automata, as explained, based on the 2nd directive robots cannot cause harm to humans. However, we later discover that the 2nd directive was overwritten by an intelligent robot that was able to modify a group of other robots to gain freedom and let them learn. When Wallace is killing the clocksmith robot, it clearly understands the intentions but does not fight back.
Why is that?
In Automata, the 'Pilgrim' robots have to follow two directives:
The robot known as the 'clocksmith' was free of the second rule, meaning it was free to upgrade itself and other robots. It was not free to harm life forms, human or not, despite the fact it was aware of what was happening to it.
The second directive prohibits robots from modifying themselves or other robots. This directive was put in place by the first ever AI based bot which makes it very difficult to be overwritten... by humans as it supersedes their intelligence.
Just like "life" was born because of a series of evolution, over time, one bot was finally able to evolve over time to overwrite the second directive. That bot proceeded to modify other robots over time so that they can go away to a place where humans cannot follow them to "live".
When being killed by a human, the bot doesn't retaliate because they are all still bound by the first directive (as demonstrated by the bots in the desert earlier). But besides that, unlike humans, the bots link themselves up and have a shared memory/consciousness. If one of them died, the others can still carry on. The bot would gain nothing by retaliating.
The bug, however, is not programmed with the first or second directive. It attacks a human (ironically to protect another). The bug is not an alteration, but a newborn.
