Ayane was
absolutely pregnant before the third reset and I will bet you any amount of money on this.
* The impregnation probably took place at the very start of that loop, in Patent-Pending -- Prisoner was in the previous loop and is a missable event that not everyone will get, but Patent-Pending is a 100% mandatory event with creampie.
* During the loop Ayane has weird food cravings, mood swings, and times of "feeling unwell" and canceling plans, which other people comment on
* Pregnancy comments take a dramatic tick upwards from her
* She has a couple of emotional breakdowns about her mother and the concept of motherhood, like on the walk with Sana in the park
* She mentions that there's something she needs to talk with Sensei about
* She calls Sensei to talk on the night of the reset and says that soon she's going to need "a lot more attention" from Sensei
* During the reset she makes it to the roof. Sensei asks Maya why she was able to get there and Maya says that she has an idea but it's so disgusting she doesn't want to say it.
* After the reset, when Sensei goes to talk to her at her dorm, she says that she has forgotten whatever it was that she needed to talk to Sensei about, and the scene ends with her saying that her stomach hurts.
* During the post-reset Ayane scene, and
nowhere else in the game, on her whiteboard is a poem about how beautiful a new baby is when viewed by its mother and how beautiful the mother is when viewed by the baby, in hex.
null125 quoted it above.
Come on, guys, this one wasn't even very subtle.