Hi! The iButton connector was designed to fit as many intercom systems as possible, but it’s not perfect. In your case, your iButton reader has a hole where our pogo pin sticks out, so it can’t make a proper connection.
You can try plugging wires into GPIO pins 17 and 18 and touching wire 17 to the center of the reader, and wire 18 to the edge of it. Some people have made a DIY adapter from a used iButton key by soldering those wires to it from the inside.
As a side note, there is nothing wrong with the center connector on your device, it’s exactly in the intended position. It specifically should not stick out of the case, as it should only touch the edge of the reader, not the central pad. In your case there is nothing wrong with the assembly of your device, just an unlucky combination of our hardware design constraints and the reader manufacturer slightly violating the iButton specification.
You can read more on how iButton works on the Flipper here: Taming iButton Keys with Flipper Zero