Right joy-con shell does not close well after replacement of joystick

I have replaced my right joy-stick according to the instructions on this website. However, when I place the plastic case back on the joy-con, I find that it does not close properly on the side of the rail. It should be tight fitting but there is a clear gap:

I wonder if anyone had the same problem and knows what can be done to properly close it. I thought maybe that the problem originates from the plastic battery case already not closing entirely well, but the screws for that part go in properly without any force.

As a sidenote: The joystick does work, but to calibrate it I need to apply force with my fingers around the joystick, otherwise it doesn’t recognize the joystick during the calibration itself.