Neat idea! I love creative little puzzle games like this and would LOVE to see it fleshed out. You might be able to get around having a separate manual by having a short tutorial level and updating the user interface. The concept is easy enough to grasp without it.
I think it'd be worth having the level be considered finished once an acceptable amount of bots enters the pipe and allows you to move on, with the option to continue the level to try to get a higher score. That would save the awkward situation of trying to finish and/or kill the remaining bots you used to move the others to the goal (this kept me locked in the first level, for some reason bots going to the left side of the screen softlocks the game).
Overall, a very strong jam entry! Keep it up!