to start, the iphone 6 is not waterproof in the first place. i would suggest against using it in the rain, that gasket is to keep the button aligned with the orifice it belongs to, while maintaining a springback feel. (not the only mechanical part that offers this.
However, being inset in the device can be a cause of a couple things.
1) Loose screws on the mount
2) The flex does not fit properly on the folded circuit
3) The glass is manufactured thicker than the standard Screen glass.
4) the screen's plastic frame is not manufactured correctly.
5) multiple of the above.
There is a possibility that the adhesive on the rubber gasket may fix your issue, but i would guarentee it, as i replace home buttons on iphones regularily, and it is usually a manufacturers flaw on the screen when i see this.
Hope this helps!