I would call Hobby Services and/or send them an email with the pictures, It really wouldn't surprise me if they sent you a different pair, without the indentation.

http://hobbyservices.com/contact.html

Of course you can get creative and try to find a way to modify the wheel pants, the gear wire, or the way the pants attach to the gear. I think personally I would fly without the pants and wait for Hobby Services response.

A fix I might try, if that's the route I was going to take, would be to attach two small pieces of bass wood vertically to the wheel pants, to create a channel for the gear to sit in. Probably two tiny blind nuts on each, inside the wheel pant, and two small screws. Maybe some epoxy as well.