When this happens to you, it is a bug - please report it as such and we will work to get them all taken care of. The name of the mob in question, and your quest (if any) are useful in tracking these down. Bonus if you can tell us the name of the ability that knocked you out.
And entrench's knockback protection only really works in pvp. Probably 80% of the strong, elite, champion, and boss mobs you fight in PvE will knock you right out of cover even with entrench active.