Ghost in the Shell: Innocence uses some brilliantly subtle visual cues easy to miss if you don't pay close attention. For example, though it's not relevant to the plot, you can tell that Dr. Haraway is a cyborg at a single glance, since she's sitting in a cold room where Togusa has to wrap his coat tight and his breathing becomes visible while wearing a labcoat with sleeves rolled up and top button open from her shirt without signs of discomfort - and her breathing, as well as Batou's, is not visible.
The intro to the 1995 animated film features the Major's body being manufactured in a factory. Or at least, we're led to assume that is what we are seeing. Much of the film's themes center on the Major's sense of self and humanity, and one scene prominently features her encountering a doppelganger of herself in passing. It's entirely possible that the intro didn't feature her at all, establishing the film's theme of human vs machine.
On the page for the original film, the Fantastic Nuke listing talks about the fact that computer programmers are as tightly restricted as nuclear weaponry. This is easily understandable when someone like the Puppetmaster could take over people's brains. None of the people it takes over are important but when you think about it, it's both Fridge Brilliance and Fridge Horror when you realize they could just as easily hack politicians, government agents, generals, admirals, anyone who would have power to use real nukes...
At one point, Batou jokes to The Major that the hacker Pupper Master seems like he might be flirting with her intentionally, and Puppet Master seems to desire to become human after becoming sentient. And by the end, seemingly a new being has been made which is the result of a mix of information between both Puppet Master And the Major. Like how an actual child is created, by being a combination of its two parents. Seems Puppet Master was able to perform one of the most human actions, creating a new life with another being.
In the opening scene, the Major jumps off a building while wearing thermoptic camouflage and assassinates a guy on her way down. Later it's mentioned that using themoptic camouflage inside a government building is strictly illegal. So the Major's chosen method of assassination may have been a form of Loophole Abuse, since she wore camouflage but never actually entered the building.
The title sequence where (what is presumably) Kusanagi's body is assembled seems to feature an inordinate amount of Male Gaze, with the camera lingering on her naked breasts and buttocks- but she also visibly lacks genitalia. She's sexualised by being given the body of an attractive woman, but she's sterile, incapable of reproduction; she has breasts with nipples, but no womb to birth a child to suckle on them. The Puppet Master wants to merge with her in order to "reproduce", creating a new being that is both of them and at the same time neither, because one definition of a living being is their ability to reproduce and perpetuate the existence of their species through iteration, rather than merely replication. Her sterility is what made this offer appealing to Motoko as well.
If the Major is a cyborg with a machine body and a human brain, how can she have periods?
They are a reoccurring mental pattern? I mean, she can't really have them due to her artificial body but her brain remembers having those and it might be calming in a paradoxical way.
Alternately, she doesn't have periods, and her claim of being on her period in the first film was just some dry humor.
In most of the continuities, the Major has been a full cyborg since before puberty, so she wouldn't remember having periods because she never experienced them. On the other hand, unlike many of the other full or partial cyborgs, aside from the dataport on her neck the Major's body is indistinguishable from a normal baseline human. If she wasn't joking, it's possible that her body is programmed to intentionally replicate having a period so she can feel more human.
