You need to get a ranged weapon to defeat it, and then use it while facing the squidbunny. Its meant to be an enemy you avoid entirely rather than just dodge like most others so i assume you just got lucky on your first run
If you're referring to the scanners, you either have futa dna inside you or some other type of parasite attached to you. You will have to either expel the futa dna into test tubes or remove whatever parasite it its before the system will ever let you through.
Did you let the Unwidow or Venus parasite fuse with your character? Most (not all) unknown contaminants can be removed either by Decon spray or C-Alpha.
