If you're trying to scan without much happening other than Apple Pay showing up, this probably means that you're scanning the wrong device at the door.

With Accessy in your phone, you should not scan the actual card reader. Instead, scan the small "A-tag" that should be situated close to the door. If you're having issues getting your phone to scan the tag, try holding your phone in different positions - depending on the actual model of your Android phone, the scanner can be located in different places in your phone. On iPhone, the scanner is always located at the top edge.