Hello Jyllianm,
Thank you for posting your query to us, first of all let me clear this that QuickApp when compiled gives you the option to download the app in your computer and you need to use your Android Market account credentials to get the app uploaded in the play store all by your self it does not get auto uploaded at all.
Secondly if you have deactivated the plugin it should be not create any problem or conflict with the website. Let me know the URL of the website that you have compiled using QuickApp so that we check that it in our end and inform you accordingly.
Regards,
QuickApp Team