I guess you missed some content than.
Here's how pregancies are implemented:
The first step to impregnating a subordinate is to tell her to stop using contraceptives.
After that, there is a random chance to impregnant her when you cum in her.
You can increase this random chance by purchasing "Fertility Booster" on Nilery. You can take up to 4 of these boosters and increase your chance to impregnate someone to 100%. Booster effects last throughout the day.
You can track the progress of the pregnancy in the Contacts app.
In the first two days, you will not see any physical changes. Between days 3-7, her breasts and belly will grow. During days 8-10, she is clearly pregnant.
For days 3-7, you will be able to have sex with her; a cowgirl and a new handjob position are available to you. However, in the last stage of pregnancy (day 8-10), sex with her is no longer possible.
After the 10th day, the pregnancy is complete and her body changes back to its original appearance. She can be impregnated again immediately after this!
After a completed pregnancy you will be credited with Mind Points. During pregnancy, the character "disappears" from the open world to keep her pregnancy a secret from everyone. However, she can still be summoned by you at any time.
Pregnancies are optional. If you don't want to see pregnancies in your game, just have your girls take contraceptives continuously.