I have 21 robots in 1 area, Near a rally point and they have been sitting there for 3 hours now. When I just picked them all up and placed then, after 6 they started to run to a enemy base but like 10 tiles in, they turn back and just idle at the rally point forever.

Would Rampant AI, or Armageddon (since they mess with AI also) mod break this mod or am I doing something wrong?

After I accidently destroyed my rally point, the group of 21 units started to attack.

yeah, the rally points can be a problem if you forget them or accidentally place one without realizing it.

don't use rally points unless you are careful.