You should be able to replace that extension flex without running into any issues. I don't know what is causing it but I know a guy that has a propensity for this happening, its happened to him twice now but I haven't seen anyone else have it happen.
I thought I had done it once but it ended up I didn't have the extension flex plugged into the home button correctly. Reseating that connection fixed the issue that time.
There is something going on with it that of course Apple won't talk about but knows about. If you do an update or restore on devices that are doing this it throws an error 53 and bricks the device. That sounds like a bad thing, but as long as you can make it look like you haven't been inside the device, they'll replace it under warranty (all iphone 6 are under warranty until at least sept. 19, 2015)