It sounds like your windows need to be recalibrated. I found some helpful instructions online by searching for Model 3 window calibration. Hopefully, that will fix it! If not, you can always submit a service ticket and have a Tesla come out and take care of it for you.
https://www.tesla.com/support/do-it-yourself-model-3#calibrating-windows
There might be a setting for this either in your car or in the Tesla App.
Also, check the 'CHARGE STATS' screen in the app. Make sure you don't have 'Time of Use' (TOU) set up there. If you do, it could be causing the issue you're experiencing.
You can still use TOU, but make sure it's only set for 'HOME' charging.