Flanking could be one culprit. Depending on what's hitting you, the enemy might be using an ability that does extra damage against guard too. If you aren't losing all that much HP on the hit, I'd suspect the later. As far as I understand it, the bonus vs. guard abilities give the extra damage only to the guard, there is no carryover to your health. If you got hit by a straight up attack strong enough to pierce your guard entirely, the excess damage would carry through to your health.
For example, you have 50 guard. The enemy uses an attack with a base damage of 25, which does 300% bonus damage vs. guard. This means there is a total of 100 points of incoming guard damage. This will destroy your guard, but the extra 50 damage will not carry through to your health, only the 25 base damage. On the other hand, if say, a rogue hit you for the same 100 points of damage straight up, this would also destroy your guard, but there would be 50 points of carryover damage to your health.
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