Got the same problem, happened from v1.1 eventually.
Viewing post in Bottle Biosphere -Living with a runaway girl- comments
if you played early version before, you have to delete the old save file. Both at the game folder and Renpy auto save.
The auto save file usually located at C:\Users\User's name\AppData\Roaming\RenPy\BottleBiosphere-1586329272
Be aware that you will lose all the game process by doing this. Since renpy doesn’t support save file update. I’m sorry about that.