Hello,
This is no bug. In this event, Emma is sitting at a table. That is why she has a little lower position on the screen. And she is a little on the left to leave the place to Ayesha's arrival who is standing, towering from all her might the tiny Emma.
As you noticed, there is other moments in the game where a girl is sitting down or changes position, with this same attempt of staging. The movements are usually explicit thanks to the text.
Staging is not always easy with 2D visual novel tools. I thank you for your concern and knowing the reason, I hope you will find the action more "readable" now.
Nico.