Either Tom and Mil are characters, or they are inanimate mechanical constructs.

Examining the latter case:

Machine B removed the connector from Machine A's port and inserted it into one on the door.

This looks fine. Notice "arm" was replaced with "port," to get rid of any hint of anthropomorphism (also, the original phrasing suggests that the door has arms).

Machine A now was again alone with its thoughts.

Something feels wrong here. Inanimate objects typically don't have thoughts.

Before meeting Machine B, it hadn't cared about that, but now it felt like something was missing from it.

Again, something is wrong. Inanimate objects don't have cares or feelings, and the thought of things "meeting" one another in this manner seems off.

That was illogical, Machine A knew, as it was still a complete robot with nothing missing. And yet, something in its circuits told it that it was incomplete. Machine A couldn't make sense of it.

Whether machines can know things or reason about them (in the same sense as sentient beings) seems like a topic for debate, but this sounds like the inner thoughts of a character, not some routine being dispassionately executed by a computer program.

You might conclude that Tom and Mil are better written as characters, and not simple mechanical constructs. Do you think of Tom as male? Call him he. Do you think of Mil as female? Call her she. Calling them "it" feels stilted to me; assigning them genders does not.

There's precedent for this in writing and in real life: read about Marvin the Paranoid Android, or strike up a conversation with a friend about Amazon's Alexa and see how long it takes them to refer to the device as "she."

Or, you might decide that it's more interesting to write about them like you'd write about any other inanimate object. But doing that convincingly seems like it would require extensive changes to the story.

Either way, in my opinion what you have now in the "it" example amounts to sitting on the fence, while the "he" example feels natural.

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