Don't stress, it's just a bruise. Those sort aren't generally a problem, just an indication. Yes, peripherally loaded horses do often get bruising at the quarters, especially with a flat trim/shoe, because IMO the quarters especially aren't meant to bear that pressure.
Your horse's toes look a little 'run forward' perhaps, but would need better pix for a real critique.
If you're seriously concerned about the longevity of your horse's endurance career, I'd seriously look into barefoot/booted. Garreth Ford & Duncan McLaughlin are 2 successful barefoot endurance riders that come to mind.