Everything is working as intended. Sector 3 final boss are B1 droids (without stacks). There is also a counter that tracks the progress so you don't have to count them manually, which is nice.
Now for the battle itself, I don't have the disks yet, but maybe Darth Maul could be an interesting option for it? If someone finds the most efficient disk combination (maybe a couple of leader's resolve disks paired with something to continuously stack attack) to ramp up his damage so that he can oneshot every b1 after a certain time passes, maybe you could get lots of kills done with auto-basic. Although that might not work if the high evasion on higher waves is a thing, since he would just miss his basics and die. Would be cool if someone with the means to do it tried it out though! I'm curious.