Right, so as I said, Usagi and Mamoru’s relationship is barely off the ground, and Usagi is used to having his complete attention (though Mamoru is totally used to having Usagi’s attention divided between him and her friends POOR MAMORU) and then suddenly Mamoru is showing this really intense devotion to this kid they barely know.

Now, Mamoru has special psychic Earth Prince powers, so he was able to sense on a subconcious level that he had a strong connection to Chibiusa and she was his daughter. Usagi does not have that, and she was also pretty suspicious about Chibiusa, though she undeniably has affection for her even at this point.

So she does not know what to make of this. The bond of a parent and child is intense and special, and Usagi sees this intensity but she can’t fathom the source. Anyone can tell you that the intense love between a father and daughter easily rivals the one between a couple, and there are a lot of examples of people feeling neglected by their partners after having children, and “jealous” of their children as a result. But Usagi doesn’t even know she’s a parent, she can’t fathom where this jealousy is coming from, all she knows is Mamoru has this really intense love for this little girl and he’s prioritizing her over his girlfriend.

She doesn’t REALLY believe it’s romantic love, and Mamoru is completely “whabutwhatSHE’SAKID” in reaction to her suggestion it might be (and also randomly finds a cup of tea to chug to get over the awkwardness) and she admits it’s irrational to think Mamoru would be in love with a six year old, but because she can’t figure out any other reason for such an intense bond due to lack of knowledge, that’s the only thing she can suggest to explain all the weirdness and pain she’s feeling. Parental love can easily be mistaken for romantic love. Usagi’s just trying to figure out what the hell’s going on, and getting a bit extreme doing it.

Basically, Naoko Takeuchi is examining the emotional impact of the divided loyalties and sense of loss a couple who has a child can experience with a couple who is NOT MARRIED AND DOESN’T KNOW THEY HAVE A CHILD. That’s pretty complex and intense for our sparkly shoujo manga (Sailor Moon is HARDCORE SERIOUS BUSINESS!) so no wonder people misinterpret such a daring character conflict.