Anyone currently in Japan on eVisa?

Hi- I enter the country last week on eVisa issued via JGA tour agency. I landed and got the print out visa in my passport (I am from USA). I use MySOS app to check in my location for two days then the app said I don’t need to check in any further. Then I also got an email that my eVisa got a notice of expiration. I am not sure what that means since I already got visa. Anyone else happen the same or know what might be happening. Thank you