Typically that is due to not properly boring the brake for the caliber. MANY brakes are shipped with a bore for .223 or similar small bore and it is left to the gunsmith installing it to properly open it up. This pretty much cures misalignment and gets you proper bore for caliber. That or just some REALLY horrible thread jobs. Either way as long as the bore of the Brake is opened up to about .020" larger than caliber you should be alright, but it's still a good idea to check before shooting.
You can pretty much eyeball it and see if there's enough misalignment to cause a strike. Ie if looking from the chamber down the barrel, you should not be able to get enough angle to see much if any of the Brake's baffles and still be able to see the full daylight through the bore of the barrel.