Scrimmages are situational and most of the plays are used to shore up the areas in which one side of the ball is considered weak or to shore up the areas which are most likely to be tested by an opponent. It makes sense that attacks against the weak points are going to be successful a higher proportion of the time. Since one of the weaker areas of our defense is the backfield (lost 3 of 4 starters), that's going to be addressed fairly relentlessly. They're going to be facing a lot of deep passes and in the process of learning, they're going to give up a lot of yards.
But, that's the price of getting better. Hopefully by giving up all those yards to our offense, they won't give up as many to their opponents. At the same time, it's also helping our offense to get the work on the deep passes.