The Gemara brings the Pasuk that G-d cries in the hideness. Then at the end the gemara says that he cries for the Bais Hamikdash in the inner and outer chambers. But there is a Machlokes in the Girsa between Rabeinu Chananel and Rashi as to where G_d cries for other things besides for the Bais Hamikdash.
Rashi Learns that he cries only in the inner chambers and not in the outer chambers. The reason Rashi says this is because the Pasuk that the Gemara starts off with seems to indicate that he cries in the inner chambers in hiding so this was simple to the gemara but the chidush of the gemara is that for the bais hamikdash he even cries in the outer chambers.
Philosophically this is very difficult, for we know that everything that happens is for good. So we understand that although things might look very bad on the outside in the inner core its all good as the Pasuk says "oz v'chedva b'mkomo". This is why Rabeni Chananel learns that usually the cry is only in the outer chamber. This I took from a discussion that goes more in depth into this with a mystical depth that is beyond me.