I think this is just a demonstration that the monster manual is a little bit sloppy in places, and certainly hasn't been playtested thoroughly-
One big example is that the black dragon can create a cloud of darkness that only it can see though, which is sustain minor, and recharges. This effectively means it has +5 to all defences, and +2 to hit, over and above its stats.
When writing a dungeon you simply have to check the monsters you run- compare them to the DMG, and to a few similar monsters. Also think how they'll do against the party.
In particular, be wary of any powers like the cloud, which are effectively a bonus to hit and damage. Also consider conditional bonusses such as those of the guard drake- If the party cannot do much about them, or they are in play almost all the time, they should be treated as part of the monsters' regular attack and damage.